Just wanted to make a couple observations...
One, respect to the writing staff who came up with a war and a revolution that is fleshed out enough to cause emotional reactions among fans. There are supporters of both sides, and most agree that the situation isn't black & white.
Secondly, regardless of affiliation, it cannot be denied that many of Ulfric's supporters are radicals. They dislike anyone who isn't a Nord, native to Skyrim (kind of reminds me of a Histler-esque mindset...blonde hair, blue eyed protestants were favored) and many absolutely hate dunmer.
Even if Ulfric is the greatest humanitarian alive, his victory ensures the prominence of such a hateful mindset, and that simply isn't acceptable to me. Should he win - A) He'll now have a shattered and divided Skyrim to try and rally against a Thalmor presence who will surely use the opportunity..B) Have a shattered and divided Skyrim who's hatred breeds, and grows to the point where its dangerous to be any race but Nord...and C) have a shattered and divided Skyrim who ISN'T receiving aid or finance from ANY outside source. There would be no petitioning the Empire to send food or supplies should the Thalmor decide to seize Skyrim in the aftermath, as well as having no allies on three different borders. Basically, in a huff that stems from RACE and RELIGION, and a desire for political power, Ulfric has put Skyrim into a position to simply be the last of a crumbling empire. There is no hope for victory with an Ulfric victory...all hope for Skyrim is lost.
Anyway, the beautiful thing about this story is that the same argument can be made that a weakened Empire cannot defend Skyrim from the Thalmor, cannot afford to support Skyrim in times of struggle, and ultimately pave the way for a Thalmor takeover of Tamriel. I think, really, either way you cut it, Skyrim is kind of doomed.