Grey Jedi: I think Jedi like Bindo were really Grey but not "neutral." I think Grey is still good or bad: Bindo was grey/good Kreia was, I think at one point, grey/evil. But neither one would do things like give away the Ebon Hawk or adhere strictly to the Jedi Code, nor would they kill in cold blood. I think it would be cool to have a "grey" side: but it isn't neutral, it is still good or evil, merely less idealogical.
What should be in Kotor III: I like a lot of your various ideas, but just remember that Kotor II seemed to try to do too much and had to get cut down. It could have been better plotwise if they had been less ambitious about putting in all the bells and whistles. Kotor I with a new good plot is my idea of a good new game.