Ummmmmm.... so the Empire is like totally the way to go!
I loooked up some of the lore and Skyrim is way in deep, the Second Aldmeri Dominion and other great powers are not going away just because someone a bunch of stormcloaks kicked the Empire out of Skyrim; they are made up of multiple land with more resources and peoples than Skyrim ever could. A decade or two without the empire, Skyrim will get STEAMROLLED by outside forces.
Plus, if you aren't a nord, you are a hypocrite. Stormcloaks are "Skyrim for the nords!"... So if you are a nord, go ahead I guess. >_>
Oh and umm, I killed Ulfric... and like after the final boss he wandered out of the mist in Sovngarde... I killed him and he went to heaven, Totally cool!