I see what you mean. To put it in simplistic terms, I have a hard time enjoying live music sometimes, because music is the one discipline that I have spent most of my life studying in depth, and that knowledge sometimes gets in the way (I notice intonation, rhythm, and other problems more clearly than others, and of course there are stylistic biases as well). Sounds like I liked KOTOR II's plot because, having not really been a student of general philosophy (other than a required course in my college days) I didn't notice the conflict between the various schools of thought.
Again, however, I think my enjoyment of KOTOR II really came from my own character's development. By the end, I felt I had developed a true Jedi rebel, someone who didn't believe in the Dantooine Council's pacifistic stance, yet still felt that they were in the light side of the force (because the game never penalized me for playing in this manner).
Here comes possible spoilers!
I would agree that, in hindsight, the story was a bit convulated. I felt the resolution was OK because I strongly felt there would be a KOTOR III, and so I expected a bit of suspense a la Halo II's cliffhanger. I liked the idea of having my own core group of Jedi Knights that would be the foundation for a new Council, and seemed to think that was resolution enough.
Plus, and again, plot spoiler coming, I really, really enjoyed the way Ed Asner's character bit the dust. Extremely satisfying, as I consider both the character he voiced and the man himself to be a pompous windbag. (-:
-Rob