You have to think about what will happen after the rebellion. Plenty of kingdoms have been raised on good principles but have fallen apart due to poor structure, poor laws, resulting wars etc. The Thalmor are inevitably going to try conquering Tamriel, so which side would be most ready for the war?
From prior knowledge, we know that the entire Empire's army couldn't stand against the Thalmor, the only thing that saved the Empire was the White-Gold Concordat, and if Skyrim became an independent nation, they would be even less likely to succeed against the entire Aldmeri Dominion. Militarily, neither the Imperials or the Stormcloaks have the means to defeat the Thalmor, but a unified Empire would have a much greater chance.
Imperials: 1 Stormcloaks: 0
Thalmor aside, that brings me to the issue that most people here are concerned about: which side is "better," or, "has better morals."
The Imperials have changed since the good ol' Oblivion days. There's no longer a valid basis for the Empire's monarchy. When the Septim's were in power, they literally had a divine right from St. Alessia, they were the only ones who could light the Dragonfires, and they were direct descendants of Tiber Septim/Talos. When Martin died, that ended, instead, a new emperor was chosen from among the High Council; an emperor without divine right and chosen without popular sovereignty; our society would frown heavily on such a government, imagine how the citizens of Cyrodill feel.
I think the similarities between the Imperial armor and the armor of ancient Roman legionaries are too numerous to be mere coincidence, for one, it gives an instant connotation of evil to players who remember the Legion of New Vegas, and it also brings to mind the declining years of the Roman empire when leaders like Caligula and Nero slowly brought the empire down on itself; I'm pretty sure the developers did that on purpose.
The Stormcloaks, on the other hand, are a bit more difficult to analyze, I can't think of any historical analogues to compare them to, and all we have for reference is what they stand for and who their leader is.
The priorities of the Stormcloaks are pretty simple: Skyrim independence and legalization of Talos worship. In practice, the Stormcloaks have taken their nationalistic ideals and turned them against outsiders and foreigners--my first thought is of the Dunmer woman being harassed in Windhelm--really, that's no better than the stigma against African-Americans in the beginning of the United States. Unless Ulfric comes out and declares--and he might, I haven't finished the Stormcloak campaign--that all foreigners and non-Nords are evil, than I don't think we should worry too much about the "racism" of the Stormcloaks.
Imperials: 1 Stormcloaks: 1
Take your pick, you can bet your money on a dying nation that can probably withstand the coming war, or a nation that may or may not have risen to the point where it can withstand the coming war.