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.
Hopefully, considering (i) the backdrop of the civil war, and (ii) the map on the Bethesda Studios wall that revealed REBELS based at Windhelm and EMPIRE based at Solitude, there is some likelihood of a more dramatic main quest where the player must choose which side of the civil war to support.
Some have argued against any multiple endings because they want their playthrough to be faithful to canon.
Personally, don't care whether any particular playthrough of mine diverges from whatever Bethesda determines to be the "canon ending" of the game, since I will play the game multiple times, making different choices along the way.
IMO, having player choices dramatically impact the world and the game's ending trumps fidelity to the literary canon of TES lore any day.