I expect that the civil war ends when Alduin comes by and blows crap up, and that way the game will end on a single path.
I've actually been thinking about this a lot- choosing a side in the civil war can easily be solved when the war ends without result to combat the rising influence of the dragons. This is more likely than actually ending the story in different ways (two or more) and having another Warp of the West incident- which I think you can get away with only using once in your lore anyways...
I really hope they don't make us choose a side. Or if they do, they add a middle faction or two. I know my characters wouldn't fight for either Skyrim or the Empire.
I also agree with this- my characters would probably remain neutral, but if they had to side, I guess it would depend on my style of character. If I were playing a Dunmer or an Argonian, who have historically been distant in their relationship to the Imperial system, I might side with the secessionists. If I'm an Imperial, however, this is less likely to happen. It all depends on the character, not my own objective viewpoint. Personally, however, I would side for the resistance. From what I'm hearing about the post Obvlivion Crisis Empire, they've become more corrupt and aggressive than before- and I was already ill at ease with them over their continued occupation of Argonia. IMO