Maybe replying to an already long thread is pointless, and maybe since I haven't read 1/10th of the ideas already posted this is a waste, but...
I really think the idea of having a secluded starting point (Peragus Mining Facility) for KotOR 2 was great, and having the PC choose what Revan was (M/F, LS/DS). I would hope that something similar to this would happen in KotOR 3. To slim down coding you could simplify it some, where you could say what Revan was, then the Exile was exactly opposite, or same alignment but different gender. However, I would really hope that you could choose the alignment and gender for BOTH Revan and the Exile, and that this would change how the game played.
The development could easily go through the roof with the decision affecting too much of the game (choosing gender/alignment for both of them = 8 different combinations total), however with more differences comes more REPLAYABILITY FTW!!!!