I won't restate all the information I already presented in the 'Now that Ulfric is High King...' thread but I will chip in my two cents here.
People seem to be focusing on the moral backdrops between Stormcloak and Empire more than the military reality of the situation. And that is, no offense, naive. Should religious freedom be allowed? Yes. Is Ulfric's rebellion based on something worthwhile? Yes, actually. Should the Stormcloaks win? No. And here's why.
The Stormcloaks might be able to consolidate Skyrim and defend themselves from an attack by the Dominion directly. But if the Empire loses the Skyrim province they will lose one of their single greatest assets. Nords. Nords are some of the strongest and fiercest warriors in the Legions. The Empire knows it. So do the Dominion. That's why the Dominion is fueling and manipulating events into this war in the first place. You may think Ulfric is fighting for the freedom of his people, a hero of Talos and so on. And even he believes that. But the simple truth is that he's able and positioned to do that because the Thalmor arranged, manipulated and worked clandestinely to get it to that point. If Skyrim becomes independent the Dominion will be one step closer to marching into Cyrodiil. And while the Imperials could give them quite the bloody nose, without the ability to call on legions from Skyrim the Empire will fall. Unless they can inspire the oppressed peoples of Elsweyr and Valenwood to begin open rebellion.
Ulfric Stormcloak is a good leader. He is charismatic. He is passionate. And the fact that after all this time he has honored and continued the arrangement between Windhelm and the refugee Dunmer is evidence that he is not a Nord supremest. He has a pro-nord agenda, but that doesn't mean he's a psychopath. His 'our side or dead side' policy is extreme. And if he has any weakness it would be that. BUT it's not necessarily malicious. When trying to shift a government into new hands it is advisable to make sure dissent is cut out early on. Cruel but true. All that said, let's face reality. Ulfric wants POWER more than he wants the liberation of Skyrim. The average Nord still believes in Talos. And many of them continued to worship Talos in the privacy of their own home. You'll notice that the Talos priest SHOUTING anti-Thalmor messages and praising the mighty Talos in Whiterun goes day in and day out without a single Thalmor coming to get him. Why? Because Jarl Balgruuf keeps them out of his territory whenever possible. What Balgruuf doesn't do is raise an army behind a pro-Talos facade. Ulfric's actions have made it HARDER for Nords to practice their religion. Not easier. And he knows it. The Thalmor taking Talos worshipers has NOTHING to do with Talos anymore. They're using it as a way to agitate the populace of Skyrim and fuel the war. Each Talos worshiping nord arrested means two family members joining the Stormcloaks and not the Empire. Ulfric isn't just working to free skyrim, with the Thalmor's manipulation he's also steadily nibbling away at the Dominion's only threat. Whether he knows it or not his lust for control is ultimate aiding the agents he hates most.
So why Empire over Stormcloaks? Because anyone with half a mind for military and political analysis can see what's happening here. The Stormcloaks may be good for a MINORITY of Nords who are not content to worship Talos in the privacy of their homes - it should be noted that most IMPERIALS are hinted to still worship Talos quietly as well. But the Empire is good for EVERYBODY that doesn't want to be a slave to the Aldmeri Dominion. Valenwood and Elsweyr are only working with the dominion on the governmental level. The rich and prominent members benefiting while the common people are little more than slaves and second class citizens. The Empire is their hope for eventual freedom. But the Empire needs Skyrim to succeed. Anyone who helps the Stormcloaks may think they're fighting for Skyrim. But whether they know it or not, they're fighting for the Aldmeri Dominion.
