From what I've read, Chris Avellone sort of went into it with the purpose of inverting most of the standard star wars tropes. Kreia was pretty much his personal commentary on how silly the entire light side/dark side dichotomy is.
My favorite part about the game (apart from Kreia) is how he retconned Revan's character into being far more interesting, by introducing the whole "distinction between a fall and a sacrifice" concept and implying that Revan had some ulterior motive which mandated his "fall." I really wish I could have seen where they'd have taken KotOR3 along those lines. Of course, BioWare decided to **** all over the whole thing with SW:TOR, which reduced Revan to a simple, uninteresting character again.
In KOTOR Juhani actually tells you Revan wasn't so bad, and he started out acting for the greater good, so I think you're misrepresenting KOTOR Revan a bit. Sure, Obsidian expanded on that idea.
As far as the story, yes K2 is better in the beginning, but then it gets very muddled. The point of KOTOR wasn't the story anyway, it's was exploring the Star Wars universe, and they did it better than any of the movies IMO.