I'll probably get slammed for this, but I would personally love to see good ol' Luke Skywalker be the protagonist in TFU 2. The story would be easy to come up with.
I think Luke has the perfect mix of massive power and unstable emotional contraint to be a character that continues to struggle with the darkside.
It could involve his efforts to restart the Jedi Order. I would love for him to discover, during the adventure, the apprentice's history.
There's potential for good story telling, and since it's post ROTJ, the environments are limitless. And we could still kill stormtroopers (there were factions that were still around).
Personally, I would like it if he came upon a unknown secret imperial facility where he discovers that the Emporer had cloned the Jedi Council, then raised them to serve the darkside. In the course of that first level, the council clones escape from this secret facility and go throughout the galaxy... then Luke has to track them each down and stop them. Each one could have his own batallion of clone troopers he commands... which would provide the fodder.
Seeing Luke go toe to toe with Mace, Yoda, young Obi Wan, and ultimately a young clone of his own father... I think that could be fun... and I think there would be cool story possibilities... like, maybe some of the clones overcome the darkness and end up joining Luke (thereby unlocking them as playable characters).
Anyway, I digress. That's what I'd like to see.