I'm just past the ship, so I can't judge the game yet. It does have two things that I really hate though, although they aren't unexpected:
(1) In-game tutorials. It just ruins the immersiveness of any game, especially when an NPC breaks character and starts telling you to "click the right mouse button to perform free look".
(2) Pause n' Play combat. I really feel that if a combat system is in real time, the options and controls should be appropriate to real time, ditto for turn-based. I don't want to play an FPS in turn-based and I don't want to play a deep combat system in real-time. Pause n' Play is just barely tolerable for me, and so far it's been a big factor in lessening my enjoyment of every Bioware game and makes me stay far, far away from any RTS game.
I don't doubt that other things in the game will make up for it, but these two things irk me pretty badly. On a lesser note, the d20 system just doesn't seem to mesh with Star Wars for me. When I see d20 I think of D&D, and it just makes me think that KOTOR is just another Bioware D&D game with a Star Wars skin covering it.