User blog comment:DarkSaiyanMitsubi/Empire or Stormcloaks?/@comment-1786741-20121010075951/@comment-3492791-20121011061920

Wronger than can be.

The Dominion controls the Empire through the White-Gold Concordat. Any attempt to violate the treaty would cause the Dominion to attack. Thus, until the Empire is in a powerful enough military position, they are under the influence of the Thalmor.

If Skyrim became an independent state, they could not control anything that goes on within it (at least not openly). This makes an independent Skyrim a threat. Not to mention half of the Stormcloak Rebellion/Uprising motive is a hate for Elves and the Thalmor. The first thing Ulfric said they are going to do after winning the war (or second after rebuilding or something) is go to war with the Thalmor. The nearby independent Hammerfell may even join them. Maybe if the Empire sees that the Allied forces stand a good chance against the Dominion they may try to join the Alliance (if they haven't been totally demilitarized by the Dominion by that point).

The Dominion gains by keeping Skyrim under the banner of the Empire, since they retain the ability to openly operate there.