Now that we know that the next game will be KOTOR 2, here's some suggestions:
From the mag scans, I read that some NPCs hate the PC hand developed in the opposite way in terms of Light/Dark side. If the PC's a goody Jedi, some characters should be pretty bad by the time the game goes on. Naturally the PC may try to convince the evil NPC(s) to return to the Light side.
Pls have the NPC be so evil (or good) that basically they say that not everybody can be changed, and it's their decision to be the way they are. Maybe the NPC then leaves and comes back to fight them etc. Basically the idea is that not every NPC will have a "feel good" group hug at the end of the game if the PC goes Light side.