Firstly, it would make the outcome of the Civil War a moot point. Obviously, it's going to be awkward as hell and just impossible to keep Skyrim under the control of either the Nords or the Empire. This way, no matter the result of the Civil War that the player chooses, TES VI would make sense. It's better than just forgetting about Skyrim.
Second, it would really make the Thalmor look like the ultimate bad guys. They need proof of their power, so how's about taking away the beacon of Mankind: Their homeland. It makes sense.
I think that this would work really well in the next game, where the Thalmor are without a doubt the bad guys.
It's just a short, quick thread. I know. But share your opinions regardless!