this is just my two cents but
1. Massive Jedi/Dark Jedi vs True Sith battles
2. More indepth romances
3. Cutscenes that show stuff about the character's past
4. The choice of starting out/joining a sith or jedi academy
5. Start as an apprentice and have your master killed or something while you are off on some planet taking your trials
6. New ship
7. More depth to the party members like Kreia, some of you probably didn't like Kreia but she was a well written character IMO