Personally I am pro-empire as I think a strong empire is the best chance of defeating the Thalmor, but that is not to say the Empire is without its problems, especially in its post-Septim era
The Empire is in decay. Cyrodiil needs to work with people on equal terms or they'll never pick up enough support to fight the Thalmor. That being said, Hammerfell gave the Thalmor a serious ass kicking. I have no doubt an alliance against the Dominion would be able to defend itself.
Ulfric may have his flaws, but in a time of war there likely isn't a more experienced and capable warlord- the kind of leader the alliance would need its members to be if it were to go toe-to-toe with the Dominion. I have a hard time envisioning him not getting buddy-buddy with Hammerfell if he manages to seize Skyrim.
As much flak as it gets, I think Bethesda did a phenomenal job making this a tough and controversial choice. Both sides have their merits and flaws.