In the Q&A it was said that the story is rather linear, which means that we probably won't be able to pick sides. Now, yes, I'd love to be able to fight for both the Empire and the rebels, but it's one or the other. Why? Because they can't have you be able to do both, because in the next game (or books, too) they would have to go with just one thing, not both. Think about it like this, if in Oblivion you could join Mankar Camoran and help him take over the world, Skyrim wouldn't be happening. That's something pretty big, it's not like people can just ignore or forget it. Sorry if this has already been brought up before, just a quick thought.
well one way they could solve that is making the sides both neutral type
like there is no bad guy and they both fight for what they belive is right and not taking over the world
that way the conflict would stay in skyrim and could then not really affect the other provinces
that is if they base thier next game somewhere else in the empire