Imperials. Reasons as follows:
1. While Ulfric's cause (religious freedom) is just, I'm suspicious of his motives. Until he started the war, the Empire was only giving lip-service to the Aldmeri's ban on Talos-worship. Indeed, Elsyf (the Empire's favorite jarl) and Rikke (the second ranking Legion officer in Skyrim) both seem to worship Talos themselves. Ulfric's actions forced the Empire to change that stance. In essence, he's fighting to solve a problem that he effectively created.
He was thrown in jail(before murdering the high king) for worshiping Talos after the Jarl of Markarth agreed to look the other way while Ulfric and his band worshiped Talos. If free worship wasn't a problem before that, he wouldn't have needed to demand it as payment for liberating the Reach from the Forsworn. The Thalmor found out somehow that the Jarl was letting people worship Talos and threatened to send an army to the Reach(which the Imperials would allow through their territory because they were enforcing the White-Gold Concordant).
2. The Aldmeri have no reason to care who a bunch of mere humans a continent away worship. UNLESS they're trying to fracture the Empire. The fact that they consider Ulfric an important asset lends credence to this statement. By "liberating" Skyrim, Ulfric is playing into their hands, turning a united empire into a bunch of isolated and easily conquerable provinces.
He is considered an asset because he ties up the Empire in Skyrim. The Thalmor don't want either side to win, and this is all mentioned in Ulfric's dossier. Tullius is as much an asset in this instance as Ulfric.