I'll take a stab at some contructive criticism.
I thought KOTOR was pretty impressive though I set it down after one play.
I agree with Shadowpaladin's observation, the major twist only has it's full impact for a certain percentage of players looking at it that way I guess you could question the desicion making during design, though I wouldn't say the plot was bad or poorly don't after that item.
In terms of wishfull thinking I would have like more of a throw back art style, all the humans especially looked like the new star wars, clean, neat and bland.
Grooming, costumes, and types of faces could have been better and more atmospheric, taking away lightsabres and familiar types of aliens this could have been any campy sci fi visually. Darth Malak and Bandon especially have very corny appearances with their chest and shoulder enhancing armor. Between their armors and corny toughguy lines, the only antagonists that successfully represented any sort of threat or sinisterness were the dueling leaders of the sith academy.
Malak is a very poor villan, probably one of the worst on reflection.
Other than those things I consider the game solid and enjoyable and look forward to what this team will do with the property, assuming the inuendo holds true.