I love moral choices in RPGs because I hate being railroaded into role-playing something I find replusive, even if it's pretend. That's actually the reason I dropped Dragon Age: Origins, an otherwise decent game.
Before we go on, I want to explain something. The reason I've never complained about moral railroading in JRPGs is because those games usually don't give you story choices at all and they don't have you make the player character at the start. If the game isn't trying to sell the idea that the player character is "me", then I don't mind being forced to guide them to do immoral things. I only complain in that case if the rest of the story is portraying them as unambiguously right. So I'll focus on WRPGs for the rest of this article.
(The definitions of "JRPG" and "WRPG" vary so widely depending on who you're talking to that I don't think it's fair to say any definition is "correct". For my purposes, the difference is that WRPGs have a main character that is supposed to "be" the player, while JRPGs have the player controlling a writer-made character.)
Continuing from the beginning, yes, in general, moral choices in RPGs are a good idea, but the ways they're usually implemented make them far worse than railroading. The most obvious problem, and I think a lot of gamers can agree with me on this off the bat, is how thoroughly white-and-black they usually are. You usually have two choices in a console RPG: one extreme lawful good and the other extreme chaotic evil, or worse, strawman chaotic evil. For example in Star Wars: Knights of the Old Republic II, I was approached by a beggar who asked for money and my only two options were to give him money or say "get out of here before I kill you" - no neutral choice. It was especially frustrating for me because that game was the first time I was trying playing a non-pure good character in an RPG. I was trying to be sort of chaotic neutral. But no, I could only be Jedi or Sith.
More than just not offering any shades of grey, I think RPG developers are missing the point of moral choices. "Good versus evil" as a recurring dichotomy doesn't fulfill the point of offering choies; it doesn't solve the railroading problem with player-inserted story games that I discussed in the beginning. Morally ambiguous situations are way more interesting, and letting the player choose what they think is the most moral option without shoving a judgement in their face is the real way to get off the railroad.
And I understand why AAA writers do this. Offering every option a player could argue for in a complicated situation is really expensive, so they want to steer away from controversial issues in their stories to minimize the number of players who feel the way I do, and substitute the worthless "would you like to save the puppy or torture the puppy?" choices as a superficial form of "agency". It makes sense as a business decision. But it really hurts their storytelling.
Also, it's basically giving yourself an impossible task to write an overall plot that works for both an extreme good and an extreme evil protagonist. For an example of this point, lemme look at a common situation from Star Wars: Knights of the Old Republic (the first one). In this game, you frequently wipe out a group of enemies and then someone who was forced into being their chef or something begs you for mercy. You can spare them for light side points or kill them for dark side points. Except that most of your companions are decent people and wouldn't stick around if you were going to kill innocents. So, in some instances of this sitation, like in the Black Vulkar base, picking the dark side option merely prompts one of your companions to say "wait, this person isn't a threat, we should let them go" and then the person thanks you for your mercy and leaves. Who the hell thought this was a good idea?!? It's incredibly maddening to dark side players since it not only makes a false promise that they can choose this but then completely shits on their agency as they're forced to submit to their companion, and it still breaks the believability of your companions because they still know that you tried to kill an innocent person, so they would still betray or leave you or if they were good. But even if they hadn't botched this situation so badly, the point is that there's no good way to make a plot that works for both an extreme good or extreme evil protagonist.
Sure, offering legitimate moral choices is more expensive as I've admitted, but if you're a AAA studio then you should be able to handle that if you waste less time writing these dumbass false choice situations. And there are plenty that are not that complicated. Even the stock "do you spare the defeated enemy mook whose actual level of guilt is uncertain?" situation is easy to implement, easy to portray neutrally, and widely applicable. At the very leaast they should acknowledge the ambiguity that's already there (by not shoehorning in a judgement on a very two-sided issue, or providing additional options when it's trivial to do so, like in the beggar case above).