Well, my character will most likely end up siding with the Stormcloaks for a few reasons.
For one, ever since the Empire turned their backs on his native Hammerfell, and his father perished in the ensuing war, he has despised the Empire. The attempted murder of him at the start of the game was the final straw.
Secondly, the Stormcloaks remind him of his brave folk standing alone against tyranny and he knows that Hammerfell succeeded, why can't Skyrim? Besides, can you imagine an alliance between Hammerfell and Skyrim? Maybe even High Rock will join it and turn it into a triple alliance, as once Skyrim is independent I doubt High Rock will remain with the 'Empire'. The Thalmor would have a much tougher fight against several, strong, spirited independent countries rather than an Empire ruling simply through strength and order, and with a lot of dissent.
On top of it all, the whole "Stormcloaks are racist!!!" debate doesn't really matter to me. In a world like this, plagued by wars, banditry and greed, it is unavoidable that racism thrives, but I like that to be honest.