I'm more concerned about the combat system then the story, I played KOTOR 2 the other day and was bored out of my mind by the combat even though i wanted to play it. If they can make the combat more fluid and retain the RPG elements such as casting that would be sweet. As far as powers it would be nice if they could compound the powers, its way to cumbersome to try and use all the powers during combat. For example, combing powers like two and three at a time as you level, master the force and comand multipower force acts like force wave/lighting/kill.
As far as story I hope that they can continue this story line and not culminate it like the trend seems to be reinforcing. I do agree the story needs to progress and make a dramatic evolution in this edition, but it should not cut itself off. I think they can take the story in the direction of the outer rim and explore a universe that is untouched. For example this universe can exist independently without messing up the cannon of EU, so these jedi in this region can explore new powers and other things that are exposed in the EU without messing up the timeline. I think this edition of KOTOR could have a unifying force theme where Revan and the Exile work to destroy the original rement of the sith but with competing idealogy (you decide the fate of the force). Will you follow the dark side or light side or will you unify the force and bring "balance". Of course this sounds like a cut off to the story, but termoil is easy to create. I think the three path would provide alot of replay to the story.