You really hit the nail on the head there. KOTOR 2 was the deepest Star Wars story I've seen. I'll go as far as to say that it is my favorite Star Wars story I've EVER seen.
I'll always be a Revanite, but KOTOR 2 is where it's at.
What's great about KOTOR II is that they made a story that wasn't normal for Star Wars. It was very dark and challenged what you thought of Star Wars and everything surrounding it. At the time of its release, you didn't normally see something like that occur in Star Wars. Obsidian did an amazing job and made KOTOR II my favorite RPG.
I think Kreia kinda made the story though. While Nihilus was the main focus of the story, the main bad guy, Kreia really made the game great.