Quote Originally Posted by Vyrerus View Post
The thing is, is that the Empire is actually against the Thalmor. They just don't have enough power yet to stand up and fight them. Ulfric is an opportunist trying to seize power over Skyrim, and had already lost if not for Alduin interrupting the execution because of the Dragonborn.

Basically, siding with Ulfric is condemning Skyrim to independent rule by someone who has already proven they can't even take on one legion of the Empire without you. They will never stand a chance against the Thalmor.

Also, the decision to execute the player was commanded by an individual. While other leaders were there, they weren't concerned with justice for individuals at the time, since executing Ulfric takes precedence. I don't really have any great love for Tulius, but his second in command kind of makes up for it. Do wish I coulda killed the lady that orders my execution in the tutorial. Woulda been nice!

Siding with the Empire is also a move that keeps it unified. To splinter it by trying to command Skyrim to be independent just means the Aldmeri Dominion get even more power over Tamriel.
Hammerfell was cut loose by the Empire and they drove the Thalmor out, so can Skyrim. Furthermore, the Thalmor would have to cross either Hammerfell or Cyrodiil in order to reach Skyrim. From which they then would have to maintain supply line whilst fighting against a nation that has a homefield advantage. It would be a quagmire for the Thalmor. Also, as an avid individualist I will always stand by a nation that wants self governance from a failed foreign power. Plus Dragonborn wild card.