What people keep saying about the dossier is that "Ulfric is placed there by the Thalmer to rally an internal war." Which is true! And "The Thalmer don't want Ulfric to win the war." Which is also true, however the only reason the Thalmer don't want Ulfric to win is because they want to deplete Skyrim of it's resources for as long as they can with this war.
And lets not forget the Ulfric (and the Thalmer) almost knowingly caused the return of Alduin by causing this civil war. The war was the last part of the prophecy to occur. A prophecy that they probably knew.
After the Alduin crisis, the Thalmer are the real enemy, and Ulfric's rebelion is doing nothing but helping it.
If Ulfric wins the war the Thalmer win.

I'm just bowing out of this discussion because I think my comments are getting mixed into the ones about the history of Skyrim's relationship to the Empire in TES V when I'm only speaking of the motivations of "empires" in general. 

