I also agree with General PloKoon - I'd love to be able to choose my own ship! It would be absurd to see the Ebon Hawk return again after getting pounded on Malachor.
Light and Dark side options on characters would be great. What I mean is, dark side characters if you play dark, light side if you play light. In TSL, Brianna/Mical really didn't at any point seem to be truly dark side, nor did Bao-Dur, whereas HK-47 never felt right playing as light side.