Too much to list off the top of my head, and I need to be heading to sleep anyway, so a couple notes:
- Korriban. Sure, it was a little creepy in the first game, but it was downright scary in this one. Obsidian did a great job making the place feel like, essentially, a Sith ghost town. Seeing the Jedi Master lying on the floor of the interrogation room, dead and bleeding, is quite a shock.
- Moral ambiguity. I've mentioned this in numerous threads, but I can't get over how great a job the storywriters did with it. At several points in the game, I was honestly unsure what was the "right thing" to do. Moral dilemmas in the original game generally involved a choice between a clearly good act and a large sum of credits that you didn't really need. Also Kreia's ethic of growth through struggle was a far better challenge to the Jedi belief in helping the weak than anything I saw in the first game.