I made a thorough research regarding both sides and i was fortunate to find (as expected to be honest) some documents at the Thalmor Embassy (main quest) that prove that Ulfric's motives are of an ominous sort. At the start i got the impression that the Imperials were very deceiving and that somehow they had their own agenda when in the end all they ever wanted was to unite the region. You don't see Imperials pushing Argonians or Khajiit aside, do you?

Why didn't i join the Stormcloaks? They are racist. They are a savage people who don't see the bigger picture. They claim the Empire has forbidden the worship of Talos when in reality they were forced by the Thalmor to sign the treaty. The Empire would tell you that they have no objections regarding the worship of Talos. But the walls have ears and the Thalmor are close. Even though it might be interpreted as an act of cowardice by the Empire, in reality they had no alternative. By the end of the Great War both the Empire and the Thalmor were at the brink of collapsing. A peace treaty had to be signed for the sake of "mankind". Of course this is where the Thalmor make their own agenda. And who did they turn to? Ulfric. Selling him false lies that the Empire had indeed forbidden the worship of Talos. Feeding him the very pretext to start a civil war in Skyrim. This makes Skyrim weak in the eyes of the Thalmor of course and this is exactly what they want. Ulfric is but a pawn in Thalmor's chess game against the Empire.
You can read some books to help you understand both sides. The Great War, The Talos Mistake and The Markarth Incident.
Hope it helped
