The "Mario RPGs" are a group of turn-based JRPG-style games. They have a few common stylistic and gameplay traits such as Mario being the main character, jumps and hammers being the main attack, enemies visible on the field instead of being random encounters, and less of an emphasis on plot and lore compared to most JRPGs (but still a lot more plot than other mainline Mario games).
But to continue Yujiri's article, the most relevant gameplay addition is Action Commands (or Timed Hits in Super Mario RPG, but this article will consistently use Action Commands). I found it odd that Bowser's Inside Story was seemingly used as the sole example of an JRPG that can do 'better', just because it had action commands, when every game in the Mario RPG series has had it so far, as well as other games that were inspired by this series (like the South Park RPGs and Undertale) having some sort of timing based system as well. So this is a gameplay-focused review on all the games in the series.
A summary of the best aspects of the series (just to quickly answer the "making JRPGs better" question):
Action commands. While action commands add an obvious skill element, I want to spotlight the possibility of taking no damage with defensive action commands. You'll never feel completely helpless with that as a mechanic, even if everyone is on low health, you know that the skill cap is high enough that it's not unwinnable. And they don't need to be simple timed button presses. There's a lot of potential, including typing, piano playing, and other skills that can be presented as action commands. A release trailer of Ring Fit Adventure came out recently (2019) which tied exercise action commands to a JRPG.
Don't have power creep in your equipment/customization system. Don't use a traditional equipment system that gives non-scaling stats. The concept of leveling up in JRPGs is equivalent to power creeping stats over time. So having traditional equipment (like +3 attack) is always going to feel more irrelevant the more you level up (imagine a +3 attack boost when you have 10 attack vs. when you have 100 attack). Usually, JRPGs try to patch this by having scaling equipment, but then tons of equipment are just strictly outclassed by other ones. If you insist on an equipment system, make most of the items not have flat stat gains, but instead percentage gains or have distinct abilities. The Mario & Luigi series has a traditional power creeped system with occasional distinct abilities, while the first two Paper Mario games have a "Badge" system with no power creep at all.
Don't have uninformed choices. Make calculations as easy and informed as possible, and don't add uncontrollable randomness. Most JRPG traditions blur the damage formulas so much - everything having tons of digits is almost an RPG joke at this point (look at Disgaea for that). Paper Mario still doesn't make the strides of fully displaying all damage calculations, but at least when most enemies don't have defense and when all attacks always deal consistent damage, working it out is a smaller inconvenience. And even with enemy attacks being random, a full dodge system allows a skilled player to avoid all damage no matter what. The Mario & Luigi series (and Super Mario RPG) continue this JRPG tradition of hidden damage formulas, and even though Paper Mario still hides them, the numbers are so low and the formulas so simple that it's much easier to work out.
Don't encourage grinding for expendable items. Mario RPGs have constantly 'experimented' with making limited-use ability items in some way or another, with Mario & Luigi: Partners in Time removing their MP system for an items system, Mario & Luigi: Dream Team having expendable badge storage, and then Paper Mario: Sticker Star making every attack an expendable item. Each of them encourages grinding for expendables because they're the most powerful things in each game to do respectively - even though the other games also had items, they were not the most powerful attacks. (Yes, I know that MP systems are expending a currency to attack. But it's not grinding, as unlike items, MP can be refilled easily, and therefore do not have 'grinding'.)
Gameplay milestones. For variety's sake, have advancements with big gameplay impacts. Some JRPGs with a "get X objects" quest don't give you anything new for getting one. That's a missed opportunity. The first two Paper Mario games reward a strong special attack for each X-object milestone.
Don't waste time! JRPGs seem to suffer from sluggish pacing a lot. Speed up dialogue, make minigames optional, cut all backtracking (TTYD didn't), make tutorials optional (Dream Team didn't, Paper Jam did), and save the long animations for special occasions instead of standard MP attacks. I hate to say that because they are generally fun parts of the game in a first playthrough but very repetitive if you're speedrunning or something.
You'll notice one of the things I don't have on here is gameplay variety and game balance. That's because it's kind of a "well duh" thing, and just pointing it out will not help you create variety and better balance. The way the games did that was with multiple features and additions that will be different for other games.
The rest of the article will just be pointing out successes and flaws of each specific game's gameplay, like a quick review.
Super Mario RPG (1996, SNES)
RPG stat customization has two forms. Lock-in is anything in battle that you have a choice in, but can no longer change freely afterwards. (If there's a limited number of changes you can make that can not replenish, this is also a form of lock-in.) This is opposed to non-lock-in, stuff like equipment and skill trees that can be changed at will.
This game has a system where you choose stats to level-up, which was an idea used in the later games. Each character has their own level and experience. Level-up bonuses are awarded at the end of a battle (there is no full heal for these level-ups). Each level-up gives some generic passive stat gains in level ups that you can't change (like a normal RPG), and then a choice between:
+magic attack, +magic defense
There was also a "bonus stat" system that incentivized a "balanced" build by cycling through each of the 3 choices and giving it even more of a boost than usual. A more specific guide with numbers is here (search [LEVUP]). (This is the guide I'm getting most of the more specific info from.)
The non-lock-in is standard JRPG equipment. Each character has 3 equipment slots (Weapon, Armor, Accessory), with most equipment being character-specific. It still has the problem of most JRPGs in that equipment has significant power creep and is just busywork of strictly better upgrades. The Accessory equip slot is at least interesting because the equipment isn't power creeped as much, and is not full of strictly better upgrades, and most of the Accessory equips are multi-character.
The stats are pretty standard RPG stats. HP, MP I'm calling the "limited cast replenishable currency" MP through this entire article for consistency, because well, it's a renamed mana points system. In Super Mario RPG, Paper Mario, and Paper Mario: The Thousand-Year Door, this is called FP. In Superstar Saga (1), this is called BP (no relation to Badge Points). In Bowser's Inside Story (3), Dream Team (4), and Paper Jam (5), this is called SP (no relation to Paper Mario's specials). In Paper Mario: Color Splash, there is a MP derivative system called paint., Attack, Defense, Magic Attack, Magic Defense, Speed. Not to the level of "Dexterity Stamina Intelligence". Now, "Magic" being used as a term here isn't very illuminating. It apparently is used as the attack/defense calculation for every Special attack, even the very non-magical ones like jumping on enemies or Bowser's crush attack. If I had known that, I wouldn't have dumped so many of my level-up boosts in regular Attack.
In battle, the game has a bunch of standard RPG tropes. It hides basically all the stats and damage formulas. There are 'elements' for damage that can deal more or less damage depending on resistances. And all damage is slightly randomized.
Speed is calculated with 'turn cycles'. The characters with the highest speed takes their turn, then the 2nd highest, the 3rd highest, and so on, until the last character in which the cycle repeats.
Each ally can choose between 4 ability categories on their turn:
Attack: Uses your main weapon to deal damage (a 'Weapon Attack'). While there's a lot of visual variety depending on the particular weapon you equip, there's no variety in the action command - it's always just pressing A once at a particular time.
Special: Spend MP to do special attacks or moves (MP is shared between all characters).
Item: One-use items. There's a secret action command that lets you keep the spent item to "Get a freebie!".
Tactics: Only two moves: Defend (spends the turn to halve damage taken that turn) and Run Away.
The Action Command system is slightly different for regular attacks vs. Special attacks. While Special attacks tend to have pretty varied and unique timings, attacking and defending is just timing one button press (A) at the right time. The "right time" involves two timing zones: a 'close' timing and a 'perfect' timing. Enemy "special" attacks can't be blocked (I don't know how to distinguish an enemy special attack from a physical one).
'Close' timing boosts damage by 50% if attacking, and halves damage taken if defending.
'Perfect' timing doubles damage if attacking, and nullifies damage taken if defending.
In my first playthrough, I only knew that timed hits existed, not that there were two timing ranges. Besides damage numbers, there is no indication of it, and you can't even tell if your 'close' timed attack is late or early.
Attack animations don't have the best user feedback in general. It still has the classic RPG trope of damage occuring at the end of the animation instead of when the attack appears to connect during the animation. This is awkward with stuff like Mario's Super Jump and Fireball attacks, that hit the enemy multiple times visually, but only deal the damage at the very end, giving you no indication on how the damage is calculated, or even if the number of fireballs or jumps scales linearly with damage.
There's also the 'standard' RPG awkward animations from this time that are not physically possible (like punching an enemy from far away and it still takes damage, characters standing on thin air to get into position for the animation). Also the Final Fantasy effect where boss characters seem to be a similar height to you on the overworld, but in battle they become giant in comparison to each individual character.
Paper Mario series
Super Mario RPG never got a direct sequel. Instead, it split off into two new RPG series, Paper Mario being one of them. This is my much preferred series from a gameplay perspective. It does so many things right that break fantasy JRPG gameplay traditions (as much 'tradition' as you could change of a genre that has only existed for a few decades).
No more equipment system: JRPGs tend to have power creep equipment, in which 90% of the equipment in the game is either strictly worse than what you currently have equipped, or strictly better than everything else you have so you already have it on. This game's equipvalent is badges. Each badge has its own BP cost. If you have 6 BP you can equip badges of cost 3 BP + 2 BP + 1 BP, 5 BP + 1 BP, 2 BP + 1 BP + 1 BP + 1 BP, etc. (This is what I call an Appoint system. It's not a common term in game design language, but I wish it was.) Anyway, this means there is so much more customization and build types available.
Simple stats: Max HP, Max MP, BP, Attack, Defense, Star Points (Experience), SP (Star Power). That's it, and Attack and Defense aren't even relevant stats near the beginning of the game (a lot of enemies have 0 defense). While the damage formulas are sadly never specified in game, they are 90% of the time simple to figure out (damage always equals attack - defense).
Small numbers: The game does not start at a level where your character has 80 HP and 20 attack or something. No, you get 10 HP, 5 MP, 3 BP, 1 attack, and 0 defense to start with. The game has very clear feedback in this sense.
Better level-up system: Experience (renamed to "Star Points") has a very simple scaling system. It's always 100 Star Points to level up. Every enemy drops Star Points, but every level you have, the enemies give 1 less Star Point. Every level-up also gives you a full HP and MP refill for Mario and his partner (which does make it not strictly better to have a higher level...). But the most important part is that each level-up gives you the choice of +5 Max HP, +5 Max MP, or +3 BP.
Few sources of randomness: No random spread of damage like "30-40" damage. Almost every attack is completely deterministic - there are no 'lucky crits'. Unfortunately some badges do add randomness, like Happy Heart which heals 1 HP every 1/3 turn, and Pretty Lucky which gives a small chance to just completely dodge an attack. And Power Bounce (on bosses) has its total hits capped at a random point. Enemies that have multiple attacks can also pick a random attack and target, but it's always dodgeable (in TTYD).
There are also a few things that really aren't necessarily better or worse than traditional JRPGs, but it's part of the 'series formula':
Mario's basic attacks: Instead of having one "Attack" button that's locked onto a single weapon, there are two 'main' attacks: Jump and Hammer. The Jump deals damage twice (it's better if you have increased attack, but is worse if the enemy has increased defense) but can't hit spiky enemies, while the Hammer deals damage once but can't hit enemies behind the first one and can't hit flying enemies. (Yeah, this is not really good balance.)
Partners: Mario has a single partner which is like a teammate that can be swapped out, like a Pokémon-esque system (but the partners aren't "catchable" or widespread). They have their own moves, stats and their own health pool, and can be swapped out at the expense of the current ally's turn. That means each partner has its own niche.
Special attacks: You know how JRPGs usually have "collect some number of celestial objects" as the main quest? Now every time you get one, you get a new special attack (with its own mana-like currency, SP). So many other games don't change the gameplay at all in one of these 'big milestones'.
Music: The music has been really consistently good, but this series has a unique boss theme for every one of its non-miniboss fights. Even in the later games!
Paper Mario (2001, N64) and Paper Mario: The Thousand-Year Door (2004, GameCube)
I'll use this section to compare Paper Mario (also known as Paper Mario 64 or PM64) with its sequel (TTYD) - I would be repeating a lot of information otherwise, because the games are more similar than different.
Optional commands: TTYD adds a "Stylish" command system. It's not explicitly stated, but an NPC in an easy-to-access underground area tells you about them. They're optional action commands that can be done in every attack (that isn't a Special attack) that reward you with extra SP.
Superguards: TTYD adds "Superguards", which adds a risk/reward element to timed defense. While normal timed defense gives +1 defense for the guarded attack, a Superguard cancels all damage taken, and counterattacks with 1 damage against physical attacks.
Random/duplicate badges: PM64's badges are deterministic - there is a total number of badges in the game and you can 100% to get them all. TTYD, though, lets you get badges through rare enemy drops, and there are a few badges that can be bought an infinite number of times. I think I like TTYD's system better but only to a point - it does allow you to grind to go all-in on a strategy (which is bad for variety somewhat and definitely much worse if the balance is bad).
Seeing enemy stats: You can see enemy stats, and the system is pretty standard. An early partner always has "Tattle" as a second ability, which tells you the enemy's HP, attack, and defense, as well as some strategy tips. But this does cost a turn and doesn't permanently display all info in battle (it just shows HP). I would prefer a passive system, as I think costing a turn is inelegant and incentivizes manual stat counting.
Compensating for the Hammer's weakness: With the amount of ways to gain attack in both games, and how Jump benefits doubly from attack boosts, the Hammer is just not often an optimal tactic. PM64 did this better for most of the game by giving you Hammer boosts first after Jump boosts (Super Hammer -> Super Boots -> Ultra Hammer -> Ultra Boots)
Level design: Since this is not mainly a platformer, it's more like world design. Regardless, TTYD has a bit more linear "hallway-equivalent" level design (first part of Chapter 1, Chapter 4, first part of Chapter 5, Chapter 6).
Backtracking: TTYD has a few moments of grating padding of going in the same areas over and over (Chapter 2, 4, 7), which PM64 had a lot less of.
Badge balance: PM64 is more balanced with badges than TTYD for sure. Since PM64 has limited badges, you can't spec into something that's completely unbalanced (as well as the 30 BP cap). In TTYD, everything about the "Danger" archetype is completely broken and shouldn't be abused in a first game run. For perspective, the +1 attack badge costs 6 BP, but the Danger badge that gives +2 attack if Mario's health is under 5 costs only 1 BP, so you can have +12 attack for the same cost. If you thought that was bad, there's a badge that gives +5 attack if Mario's health is 1. That's +30 attack now. The design idea of the badge was probably that 1 or 5 HP is a 'risky' position to be, but because all battles (well, if you don't get First Striked) let Mario's team go first, you can just kill them on the first turn. Even if you fail that, you could just use invisibility items, Veil (a partner ability that basically gives 1 turn invisibility), or just run away from the fight.
Mario & Luigi series
The Mario & Luigi series is a lot more consistent in gameplay across the titles, but shares a lot more with traditional JRPGs and is arguably more casual overall, but has a higher emphasis on action timing. This will compare all 5 games that are currently out - Superstar Saga (1), Partners in Time (2), Bowser's Inside Story (3), Dream Team (4), Paper Jam (5). I've put numbers after the names for readers unfamiliar with the series.
Gameplay: The gameplay lacks strategy. I mean, I enjoyed playing the games, but I enjoyed the success of performing difficult or fast action commands. If you look at any Boss Rush video all you'll see is the highest-MP attacks over and over, along with the occasional heal (it matters a bit more in this game, as all MP attacks are themed as "Bros. Attacks" which means they get disabled if one of them dies). It is impossible to make informed decisions when all the damage formulas are hidden. Most of them aren't even differentiated by status effects or anything similar, and the ones that are, the bosses are immune to anyway (like Dizzy).
Equipment: 3 slots for each character like any other JRPG. I would criticize that there isn't much room for choosing which character gets which equipment, but most of the series' gimmicks at this point have been extra characters (each game has 2/4/3/2/3 'equippable characters' respectively). Also, in later games (starting from Bowser's Inside Story (3)) there are occasional level-up upgrades that happen every 10 or so levels with lock-in bonuses, one of them being extra equipment slots.
Stats: The stats shared between games are Max HP, Max MP, POW, DEF, Speed, Stache. Unfortunately, we've got somewhat inconsistent naming across the series, so "Max MP" here is actually "Max BP" (Bros. Points in Superstar Saga) or "Max SP" (in Bowser's Inside Story). The "Stache" stat here is a combination of a higher crit chance and getting better shop item discounts, because that makes sense.
Clear damage/numerical formulas: Besides Max HP and Max MP, I still have no idea how the damage stats are calculated at all. The first game I ever played in the series was Bowser's Inside Story, and it was impossible to not notice that at the start of the game, Mario is dealing 2 damage with his jump, yet has 20 POW. Either the enemy had more than 0 defense (in which the defense value would have been a hidden variable), or the enemy had 0 defense and there was a hidden variable modifying the attack. Either case the damage formula is a black box right from the start. jdaster64's work is about the only person doing further writing on damage formulas: SS, PiT, BIS.
Seeing enemy stats: You can't.
Level-up system: Like Super Mario RPG, you gain a bunch of stats passively when you level up, but here you can choose from one of the six stats to increase in a roulette system where you have to time "hitting" a number in the roulette. These start at around 3-4 at the highest and 1-2 at the lowest, but there's also a "balancing" mechanism where you get lower numbers if you keep upgrading the same stats (1-3), and the rest of the stats will get higher numbers (4-7). This kind of pushes the player towards not "regretting" their level-up lock-in, but there was a mechanism in the first two Paper Mario games that let you swap around level-ups.
Finally, theming, again:
A gimmick per game: Pretty good variety. None / Babies / Bowser / Dreams / Paper.
Beans: Beans are permanent stat upgrades, just like you might see in Final Fantasy. Super Mario RPG and the Paper Mario games don't have them. But for some reason getting them is a big chore - you have to drill into a bean location and jump out.
Gameplay gimmicks and action commands in the Mario & Luigi series
While I said the gameplay was lacking in strategy, it does have lots of gimmicks per game that change what kinds of action commands you do. There's two main buttons as a series standard - A is "Mario' buttons" and B is "Luigi's button" by default, which I will call "character buttons".
On the overworld, the character buttons cause the respective characters to jump, but navigating through the world is a bit more cumbersome due to extra cycle commands - you can press a button to cycle through other abilities that get unlocked (which is different per game). I broke my trigger button in my first playthrough of Bowser's Inside Story because of it (they became soft and took more effort to click). Superstar Saga (1) has it the worst, with a 3-cycle of Jump/Jump, Hammer/Mini-Mario, Fire/Tickle, but also has a "switch order" button to change the cycle into Jump/High Jump, Hammer/Luigi Dunk, Dash/Thunder.
In battle, on-your-turn attacks only use the character buttons involved with the attack (and very occasionally D-Pad or circle pad controls). When defending, the character buttons are used for "counterattacks" (somewhat of a misnomer, as some attacks can only be 'countered' with a dodge and can't deal damage back to the enemy - but most attacks can counter with damage). These counters are much more animated than the Paper Mario series.
If the counter involves countering with a jump, but in-battle (and on the field, if you press R) if counterattacking. This is not like the traditional Mario games where variable holding/releasing the jump button gives you variable height.
If the counter involves countering with a hammer, the button instead 'brings out the hammer', and releasing it swings the hammer. I believe in Superstar Saga (1) and Bowser's Inside Story (3), you can't hold it out for too long or you'll drop it and there'll be a cooldown until you can bring it back out. That mechanic was removed in Dream Team (4) and Paper Jam (5), and I really don't get why, as it means there's no reason not to just hold the hammer buttons forever until you release.
With the standard A and B buttons, a ton of attacks in the whole series can be dodged too easily by pressing/releasing both A and B when an opponent is attacking ambiguously, so you never need to react as soon as you find out who is being attacked. The designers seem to have known about this since the first game (the final boss has an attack that punishes you for jumping when you shouldn't have), but it's still in there.
Okay, so here's the gameplay gimmicks and how they change stuff.
Superstar Saga (1) changes nothing (there's nothing to change). Well, it actually has a mechanic that's never used in any later game, the "Advance!" attacks. If you use an MP attack enough, an Advance! version gets unlocked, which lets you do an optional press during the attack to do a different attack (not always a strict upgrade). This is almost identical to just gaining a new attack option, but it slightly decreases menu time. So I prefer having Advance! attacks instead of splitting it up (the remake splits the Advance! attacks into different attacks).
Partners in Time (2) has Baby Mario and Baby Luigi, with X and Y as their character buttons respectively. This is probably the most action-complex of the games, as all of ABXY are used in battle. Also, there is no MP at all. Instead the Bros. Attacks act like items, being one-use. (But the game feeds you so many items they may as well be infinite use...) Functionally, the Baby characters are more like backup characters, as they do not have their own turns until one of the party members dies.
Bowser's Inside Story (3) has Bowser, with both X and Y as his character buttons. The X button is a punch (hitting things close to him, like a hammer), while the Y button makes him duck (having his shell aimed upwards as well, to counter enemies attacking from above). All his counterattacks are not contextual - he can press X or Y for every counterattack (unlike Mario and Luigi which have A being jump or hammer depending on the counter). He also doesn't have Jump and Hammer, but instead Punch (like Hammer, hits one ground enemy) and Flame (hits all enemies and inflicts Burn) as his main attacks. He also has a passive "Fury" mode that triggers if he takes too many hits (doubling damage dealt and received). Unfortunately, he does not fight alongside Mario and Luigi so there are no combo-attacks involving all 3 characters. This game also introduces badges (no relation to Paper Mario badges) - these are effects that you can activate once you deal enough damage. These were moderately customizable and added some much-needed strategy. There's also a new type of battle (Giant Battles) that were used in this and Dream Team (4), which... well, each 'turn' only has like 3 choices to it, so it's more like a cinematic minigame.
Dream Team (4) has a Dream mode where Luigi does not participate in fights as a party member (separate from the normal mode, which is pretty straightforward gameplay). Instead, Jump and Hammer attacks become hit-all attacks as well as Mario having a different set of MP moves. During Jump counterattacks, Mario can move side to side (front to back from the player's point of view) with Up and Down on the circle pad. During Hammer counterattacks, Mario can orient the direction of the hammer counterattack with the circle pad. This game also introduced "orthogonal counterattacks", which is like a sort of Crash Bandicoot-style linear hallway where the characters are running towards the screen and away from an enemy. There's also an "improvement" to the badge system from Bowser's Inside Story (3) that lets you store the effects of a full badge to use for later. This is a violation of Don't encourage grinding for expendable items - I remember constantly grinding to get 3 full badges of the "each party member takes no damage against their next 3 hits" before each boss fight.
Paper Jam (5) has Paper Mario, a party member that fights alongside Mario and Luigi, with Y as his character button. The way he works is quite different than other party members, with a Copy ability that adds 'copies' to Paper Mario, giving him extra attack and making him completely invulnerable to enemy attacks (instead of taking HP damage, he loses copies). It's pretty overpowered, as it has no cost. During Jump counterattacks you can hold his button for a longer time for a "flutter" jump. The "badge" system has also been replaced by a Battle Cards system where you instead accumulate Star Points to 'play cards' which have effects similar to badges. This has no relation to the first two Paper Mario games, these Star Points are more like another MP system. Besides having to refill Star Points (which is moderately grinding for expendables), this is much better than the badge system it replaced, since you have much more choice in what effects to do.
Tutorials: The whole series is kind of full of point-out-the-obvious tutorials, but Dream Team (4) has it the worst. Paper Jam (5) implements a Battle Guide, which I believe was also added in remakes of the previous games.
Animation time: Superstar Saga (1) had the fastest animations by far. This was then made more grandiose and time-consuming in the later games, as animations became much longer. Paper Jam (5) has "Trio Attacks" where all 3 party members "team up"... and they really should have been way more rare and powerful. The animations look great, but you'll probably see every one of these animations each like 100 times in your whole playthrough. All that buildup and you'll get some only slightly above average 250 damage at the end or something.
Story sequencing: The plot of the games are more 'realistic' from an overarching standpoint. While there are occasional moments of "get X objects", you can't explain it in full with "get 7 Star Spirits" or "get 7 Crystal Stars". The closest is Partners in Time (2) with a "get 5 Cobalt Star Shards", and even with the overdone trope of "Oh no! The entire goal of collecting X things was evil all along!", the number of shards doesn't go up one by one.
Super Paper Mario (2007, Wii)
Super Paper Mario is not a JRPG, so this article will not cover it.
Paper Mario: Sticker Star (2012) and Paper Mario: Color Splash (2016)
This series took a controversial turn when it completely changed every gameplay element for the worse, and watered down the story. In fact, you may as well forget everything you know from the "Paper Mario series" bullet points.
Battling: Imagine a typical JRPG. Now remove all commands besides Item and Run. That's what these games are. In Sticker Star, the system is dressed up as "Stickers" instead of items, and in Color Splash, dressed up as "Cards". Yet they're both completely functionally equivalent to items, being 1-use only. Some of these items are better than others (and intentionally in Sticker Star - there's Worn Out, Normal, Shiny, Flashy, Big Shiny, and Megaflash versions of stickers).
Customization: Is basically completely removed. No more level-up bonuses, no more equipment, no more badges. The only ways to 'upgrade' Mario is permanent hidden "Max HP Up" items lying around.
Action commands: Have been watered down. Every single action command is now a variation of pressing A, and many, many more attacks have the same action command. It's almost like it was designed for a phone interface or something with A being the equivalent of a tap. You can't even select an enemy to attack anymore, you can only target the front one (or all of them if the attack is an all-attacker).
Simple stats?: Kind of... all the numbers in the game are scaled about 2x what they would be in Paper Mario. A bit irritating but the numbers are manageable.
Clear damage/numerical formulas: In Sticker Star, you actually get to see enemy HP, but only as a total. You can't see individual enemy HP, you kinda have to logic it out through trial and error (there's a vague indicator of low enemy HP, if the enemy looks more greyscale, it has lower HP). But at least you get to see damage numbers, even though none of the attacks tell you how much damage they deal until you actually use them. Not so in Color Splash! They have completely removed seeing the amount of damage you deal, but at least you can still see how much damage you're taking. And while Color Splash has an effective MP system (renamed "paint"), you can't see how much paint each attack consumes, but strangely you can see your max paint cap as a number, which really is not much help when there are no numbers for anything else that uses paint. If the series continues going this way you can probably expect anything remotely resembling a number to be removed in the next game.
Level-up system: There are no levels in Sticker Star, and thus no experience system. I've heard complaints that this means there isn't incentive to battle (you get coins instead), but I don't fully agree. The reason you won't want to battle in Sticker Star is because battles are not strategic, with the damage of various items being hidden. In Color Splash, there is an experience system, but with little incentive to level-up (you only get a minor max MP (paint) increase with no other choices). TheBitBlock did a review of the game where he intentionally avoided all EXP drops and still beat the game without difficulty. That's also partially because you can find paint all over the place in maps and in enemy drops, as well as the existence of pre-painted cards, that a max paint increase only really affects long battles where you actually have a risk of spending most of it.
Busywork: The Sticker and Card menus in Color Splash are basically glorified Item menus, but since it is the whole game's method of attacks, you'd expect the interface to be good. At least in Sticker Star it's not that hard to use, as there are 15 sticker slots on a page. But duplicate items aren't stacked. And Color Splash decided to remove the page system, so the items menu is now a single line which could be 60+ cards long. In Color Splash, the amount of effort you have to expend to play a single attack is ridiculous. First you have to select it, hold the card to 'paint' it in (otherwise it will deal barely any damage), then press a "ready" button, then 'flick' it upwards. Video example and comparison here from TheBitBlock's review.
"Things": "Things" are basically "super-attacks". But they're still one-use like every other item, so they're basically items too good to use for a normal battle. Most bosses (in both games) have a certain hardcoded "weakness" to a certain Thing which is completely hidden and still requires a reasonable guess to figure out which is needed. Quote from an article from Goomba Stomp: "While thing stickers are like regular stickers in that they can only be used once before being discarded, their rarity requires you to go to the hub town to replenish them. They’re also quite expensive to restock, so it’s not recommended to be constantly using them and buying more. Since that whole process is something that’s preferable to avoid, it becomes far more practical to conserve them until you come across an obstacle that absolutely required their use. This would be fine if it weren’t for the fact that these stickers take up a large amount of space in your inventory. It’s simply not possible to carry all of your thing stickers, and since there’s no way of knowing in advance when you’ll need them until it’s too late, you’re basically forced to guess which ones will be more useful than others. This becomes especially annoying for boss fights. Most of them are absurdly difficult unless you already have the precise sticker that makes them vulnerable. There’s often no other option but to run away from the battle, go back to the Toad Town, buy some things, convert those things into stickers, then go all the way back so that the boss can actually be fought. Hardly a climactic way to end a chapter…"
Theming: I think people scapegoat the theming of these two games because they focused so much more on the 'paper' aspect, and say things like, "We don't want "Paper" Mario, we want Mario Story!". But I don't have a problem with it. The issue is the watering down of every other element that the theming is just the most notable element of the game now. There's actually a lot of creative things the developers did with a paper theme, like stacking, folding, cutting, glittering, sparkling (the Cutout mechanic in Color Splash takes advantage of perspective tricks - while a "go in the background" mechanic was used before, it wasn't done like this).
I would end this article with a summary of the games, but I already put that at the very top because that's better reader experience. :P