The Stormcloaks all the way. As Phasmatis said, they did not try to chop my dome off after they found out I was not their enemy. My characters tend to take a thing like people trying to murder them personally...
Beyond that, the Empire is done. It is a corpse that is already falling to the ground. Signing the White-Gold Concordant was an act of pure idiocy. It gave the Thalmor in diplomacy what they could not gain through force of arms. The Thalmor failed in all their objectives in the Great War. They did not conquer Hammerfell, they did not conquer Cyrodiil. They were left right back where they started when the dust settled. Except afterward they had lost an entire army in Cyrodiil, then lost even more troops in the 5 year long war they lost against the Redguard in Hammerfell. The Redguards who
fought and defeated the Thalmor all by themselves, after the Empire had thrown them aside like yesterday's laundry. Now both sides lick their wounds. However, this gives the humans the distinct advantage. For they will win a war of attrition. SImple breeding is why. 18 years after the end of the Great War, all of the human nations will be right back up to full strength. It will take the elven nations centuries to do the same. A few more Great Wars, and there won't be any more Altmer or Bosmer left alive. The humans will suffer, but will bounce back, as always.
The Empire has shown it lacks the insight, and just plain will, to fight the war against the Thalmor to its inevitable conclusion. The Nords on the other hand, are different. They still have the warrior spirit that led their ancestors to exterminate the elves in Skyrim (well, excepting those guys who took an arrow to the knee...

). Skyrim gaining its independence is just the first step in a resurgence of Nordic power. Afterward it is primed to lead an alliance of humans against the Thalmor, and wipe them out for once and all. How is that? They have the Dragon-Born after all, the obvious choice for the new High King of Skyrim (sorry Ulfric, but you aren't the dragon-slayer who saved the world). Not to mention the Dragon-Born has legal claim to the throne of Cyrodiil. That would smooth over the Nordic conquest of Cyrodiil. Even aside from the Dragon-Born, in a few years Skyrim can raise an army of Thu'um users. Ulfric is just the first. If he can learn it, there is no reason they cannot train more. Forget the Greybeards. Those doddering old fools can sit on their mountain and collect spiderwebs while they do nothing, as they have for thousands of years. With an army of Thu'umsters, the remnants of Alinor and Valenwood simply do not stand a chance. Even without them, it is only a matter of time before the weight of human numbers simply overwhelms the elves.