Many people base their choice on one of three things:
1. The way they generalize the empire. "The empire tried killing me at the beginning, so I'm with the Stormcloaks."
2. The way they generalize the Stormcloaks. "The Stormcloaks are racist, so I'm with the Empire."
3. An outcome-oriented ethics philosophy. "The empire's just doing what it has to to survive, and that includes protecting the future of Skyrim, even from within. I'm with the Empire."
I reject all of these reasons. The first and second are examples of emotional reactionism, and the third subscribes to end-justifying-means ethics. They are all based on false (or at most uncertain) assumptions. The "means" of the empire is acting like an obsequious dog at the table of the Aldmeri Dominion. If faith means anything at all, it means not forsaking faith in the face of possible destruction. The empire shows only that faith means nothing to them; this is proven by the fact that the Thalmor are free to roam Skyrim, murdering those who place their faith above tyrannical politics.
Now, maybe you agree with the empire, that faith is worthless and misplaced in Talos; then you will also likely agree that might makes right and that the empire needs to do whatever it can to stay strong. I, however, disagree, and oppose the empire, because if faith has any meaning, if it is ever a virtue, it becomes so precisely then, when politics and tyrants and the world demand faithlessness.
When Ulfric used the power of the thu'um, a gift of from the chief deity of the divines (Akatosh), to off the high king (a political rival), the notion that the Stormcloaks held a moral high ground in terms of faith fell apart.
To me, there are only two reasons he used the shout in high combat, neither of them desirable:
1.) He used it as a means to intimidate anyone who would challenge his rule.
2.) He used it out of desperation to defeat the king.
Don't get me wrong, however. What the Empire did to Talos was outright disgraceful. But it still leaves me in a state of disdain for both sides.