Has anyone considered using source material from the Republic Commando novels? Many great ideas there, including matte-black Katarn armor. The sequel game would have to eventually deal with Sev, but because the squad was part of the "bad batch" of clones that didnt take commands mindlessly, I think the squad would be able to ignore Order 66.
I would bet the story would involve the squad "hunting" jedi, but in reality, they're helping the survivors escape, in exchange for help finding Sev?
Oh, and new weapons would be nice.
No vehicle usage, it would be too much, but turrets are good. Maybe something like a remote mouse-droid, to access hard to reach areas on a level and see whats there, with a self-destruct option.