I had a very hard time choosing, this is one of the in-game decisions that I will remember for a long time.
I chose Empire, for a few different reasons.
First, the Empire NEEDS Skyrim, and Skyrim NEEDS the Empire. Without the manpower and skill of the Nord troops, the Empire will not win the second war versus the Thalmor. But if Skyrim gains independance, they can't stand alone against the might of the Altmeri Dominion.
Secondly, if Humanity is to survive the Thalmor's future attacks, (and believe me, they are coming) they will need to be united. The old cliche, divide and conquer.
Thirdly, I firmly believe that the Thalmor are right about the divinity of Tiber Septim. (No matter how much I hate those prejudiced bastards) Tiber was a great man, and a good emperor, but that does not make him a god.
I've been soundly proven wrong on that point, however, I would like to say the the Empire is just buying time with the White - Gold Concordat, when the next war happens, and if the Empire wins, then of course worship of Talos will be reinstated. I guess till then, stick it out?
While the Empire might seem to be a puppet of the Thalmor, you know, the whole concordat and all, make no mistake, shit's going to go down, and soon. The Empire will need every sword at it's disposal. It can't afford to be surrounded by hostile forces on yet another side.
No matter how just the Stormcloaks cause may seem, their demands must be rejected, for the greater good.