My first character, an Imperial thief, almost sided up with the Stormcloaks simply because they weren't trying to axe my head off in Helgen and I was completely new to Elder Scrolls. Later on, my thief ended up siding with neither, since there was no good loot to be had. Needless to say, my thief ended up focusing on the Dark Brotherhood and Thieves guild instead.
Recently, I've been using a new character of mine, a narcissistic Altmer, who is focusing on the College questline, and is siding with the stormcloaks. My logic in that alignment being that the whole Talos issue the Nords are upset about is only a means to an end for the Thalmor, and that end is their wiping the Empire off the face of Tamriel. Logically, Skyrim's independence would cripple the Empire further, and make the only remaining Empire territory besides Cyrodiil (High Rock) nigh impossible for the Empire to make use of in another Thalmor war since it's bordering Hammerfell and Skyrim, both independent after the Stormcloaks boot the Empire from Skyrim.
However, I personally feel the Empire is necessary for maintaining order in Tamriel. I see the civil war in skyrim as but a small battle in the greater picture of potential restructuring of the ruling government. Considering an Empire government promotes peace and order, I imagine a Thalmor rule in Tamriel would be a brutally harsh life for any non mer race. I imagine the Windhelm segregation would become commonplace, and the government would only act in the best interests of elvenkind.
Oh yes, I also don't care for the Stormcloaks simply because Ulfric strikes me as of a spoiled brat throwing a tantrum when he doesn't get his way. I could list numerous examples of what led me to feel this way, but without spoiling anything, all I will say is that I think he's every bit as much a smug racist as the Thalmor are.