KOTOR 3 must follow the Lucasfilm canon...which is LS Male Revan and LS Male Exile. Always gotta have a happy ending, right.
I would also like them upgrade their graphical engine. If the technology in KOTOR 3 doesn't improve with the times (and this one didn't) then it doesn't matter how great the story is...it'll be a moldy oldy.
I don't think there is a need to resolve what happened between KOTOR 1 and 2. There is a need to resolve the Mandalorian, Sith, and Revan's travels. The Exile's storyline is more or less resolved. It's basically what happens to him now, as opposed to knowing what happened to him back then. What exactly happened to Revan and Malak is more important than going over the Exile's past...the reason it's more important is if there is a presence out there that creates or indoctrinates the Sith culture.
I'd like to see Revan played as LS character, but without the mask. In each game you could see the character face that they had envisioned. KOTOR one is the balded headed character with the fu-manchu that has no other variations of his head. In KOTOR 2 it is obviously the same character that shows up on the Box. And in fact if you play through the games with those characters the wardrobes and character make-up fit very well. The other heads look silly, actually.
Game specific:
I'd like to see the ability to use more than two extra characters.
Review the force powers, rebalance them and use them as needed. There are a lot of powers there that really don't allow a character to specialize in force use, which is supposed to be the job of the Consular. Make more of the powers universal, but allow only the most potent one's to be LIGHT/DARK side specific, AND score heavier penalties unless the character had that skill and was light side...but then fell to the dark side later.
Make the light saber and component upgrading much more simpler. I like the balance of the first, and the second one however is too deep. Having a level (1, 2, 3, 4...etc) of one particular emitter makes no sense. If you can build the emitter (power cell...etc), then great, otherwise you can't. Do that or allow each individual component to be upgraded (such as a basic emitter can be upgraded to a level 2 by using a better crystal or new attachment...etc).
Mix the best parts of KOTOR 1 and KOTOR 2 together.