I debated this as well, and finally opted for the Legion. I think from a pure gaming perspective, it's irrelevant, but putting myself into the character, my reasoning goes like this ...
The Empire out of fear allowed itself to be forced by the Thalmor to ban Talos worship - to save the whole Empire.
Ulfric and the Stormcloaks are blindly racist, though fighting to retain their worship of Talos is just.
Supporing the Stormcloaks will create a divided Empire, ripe for attack by the Dominion.
Supporting the Empire is more likely to bring the Empire together, given that only half the Nords support the Stormcloaks.
Although this option appears not to exist in the game, I believe that as the savior Dragonborn, you have the opportunity to change the empire from within and fght the Dominion - to free the empire from the influence of the Thalmor and return Talos worship to the Nords, while benefitting all races of the Empire - perhaps to even become High King or Emperor? Quite a bit tougher as the xenophobic High Ing of a rebel province.
Spoiler - and I'm not happy that Ulfric is in cahoots with the Thalmor - that bigger picture is more important to me.
oh ... and Ulfric is a douche.