I'm not sure what sort of innovation you're looking for with their RPG's. I've never played Neverwinter Nights, and while I'll agree that DA:O, ME and KOTOR follow the same good/bad system and party influence mechanics, they do still feel like very different games to me.
I thought Kingdom Hearts was a good take on the action-RPG. I liked the idea of being actively involved in an attack in Legend of Dragoon and Magna Carta (though it can be tedious after while). I liked the strategic choice of Chrono Cross's basic attack where you had light, heavy and medium attacks with various dynamic accuacies and damage ratios; there was far from a single optimal way to choose to attack. I thought Valkyria Chronicles had an interesting amalgam of platforms in its combat system.
I love the whole good/evil develop your character system. It's more immersive, you feel more involved, and it helps to develop the story. Especially in Dragon Age when it gets a bit... shall we say "political"?
Personally, I find it severely distasteful several reasons.
1) The idea that any decision can be simplified as either good or evil (or whatever binary system they have) is fairly ridiculous as a concept. I'm infinitely aware of this while playing.
2) Often they tie rewards to choosing a specific path. So if I feel like being an @#%^, but I want to get the defensive armor, I have to be nice to people. "No, no, no, @#%^ in this game are offensive characters, good guys are defensive." I feel like I'm forced to play the game in a way I don't like to get the storyline, character, or item that I do like.
3) Sometimes the decisions don't make sense. I might be given the option to help out a peasant farmer, and so I choose it and get evil points because apparently he was the village thief or something. I might badmouth somebody and get good-side points because another character happens to agree with me. It makes me very aware that this is a contrived system, and it doesn't seem to make very much sense.
4) It doesn't feel like I'm really causing the story result, merely that I'm choosing it. GTA4 was a good example as to how to handle decisions that affect the storyline. In Dragon Age I was aware that I was choosing the evil option and therefore would get the evil ending, but it wasn't clear how the line connected the two.
5) It's been done far too often.
6) It often weakens the storyline. Choose your own adventure books tend to not become great classics for a reason. There are two situations that can occur, and both of them put writers in a bad spot with he story. Either a decision has to achieve a certain singular result because the rest of the storyline is dependent upon it, and so the decision you made never really mattered. Or a decision does matter and writers are forced to create two very different endings to a game. Having two very different endings in my opinion is awful. What if Romeo and Juliet had instead lived as an alternate ending? The tragedy is ruined.
But I'm scratching my head on your dismissal of Baldurs Gate.
It's probably just personal taste. I'm not too fond of D&D pre-4e, which serves as a lot of the inspiration of Baldurs Gate. I also don't like many of the systems involved in it, such as strength determining carrying capacity. That has always greatly annoyed me.