I'm not sure about adding dialogue choices for picking the gender/alignment for Revan and the Exile. Having the new PC in Kotor 3 pick who's what for both of the main characters from Kotors 1 and 2 seems a bit clunky. Then again, being able to pick can give the storyline a bit more flexibility.
Regardless of that, I'll join the bandwagon and say that Revan and the Exile need conclusions or a continuation of their stories if the loose ends aren't tied up. I say this because something should be left open if Kotor 4+ is on the distant horizon.
As for when and where Kotor 3 takes place, moving out into the unknown regions would probably remove the setting too far from the better-known Star Wars locales. Taking place during the invasion from the True Sith sounds workable. That way the writers can explore the stories of the characters from the first two games and how they dealt with the new invasion.
I prefer to not revisit the places that were included in Kotor 1 and 2, sort of a "been there, done that" mentality.
Keep the tried-and-true combat from Kotors 1 and 2. It's the Kotor 'thing' now, for good or ill.
Increase active party size to 4, but not any higher than that, though, as the PC isn't supposed to walk around with his/her own army. I'd like this because there may be certain missions/areas where one member has to be taken with the PC (as Mandalore was on Onderon), limiting the player to one choice for a companion.
I'm not a fan of missions where the player is forced from one area to the next (Landing on Onderon the first time, Sith invasion of Telos/Malachor), excepting any introductory parts (like Taris/Peragus). I like choices, so being able to run around the galaxy and delay the final battle appeals to me.
HK-47 is a must. If any character is added to the party for Kotor 3, it must be HK-47.