Didn't play too much of Skyrim, but I did do a bit of the civil war stuff. I sided with the Empire. I liked the way that General Tullius right-hand woman rationalized it (I forget her name); If the Thalmor were really to get tyrannical with the Empire, to the point where the Empire saw fit to fight back, they would need all the manpower they could muster. If Skyrim was independent of the Empire, they would probably be out of the loop of any political dealings between the Empire and the Thalmor, and the Thalmor could easily divide and conquer.
I couldn't give two shits about Talos or racism. There are bigger things at stake here. A stronger Empire is a stronger Skyrim.