Imperials. I think a principled argument can easily be made in favor of the Stormcloaks, but just as easily, a practical argument can be made in favor of Skyrim being part of the empire.
Ultimately, my choice is because my fav city is Whiterun, and choosing the Stormcloaks causes it to get damaged. Is that a good reason? Probably not, but I spend a lot of time there in each play-through and I don't want it to get damaged. Granted, in my dozen play-throughs I've probably only finished the Civil War story-line once or twice, but I digress.