Either way in the next game. Its pretty much a win, win situation for the Thalmor. Storm Cloaks win, the Thalmor take Skyrim because the Nords don't have an established government and the Thalmor won't tolerate King Ulfric as a High King. They even want the Storm Cloaks to win because after the Storm Cloaks win, and they are a small band of rebels. The Thalmor can just come in and mop the rest of them up and be declared winner. Plus the Thalmor have an Embassy already set up and are just waiting.
If The Empire wins.....the Thalmor still win since the Empire is already under their thumb. For what ever reasons why the Thalmor didn't invade is because of the civil war. But they did say that the Next Great War is inevitable even with all the countries or providences in a mess.
Either way, we'll be seeing the Thalmor in the next few games. I honestly think the Empire is done and I think Bethesda wants to show us a world where the Elves have a powerful Empire of their own.
Its good to see change come and go. But as much as I wanted the Empire to recover, I don't see them winning the next war with the Thalmor since they lost the first war and signed off their rights on the White - Gold Concordat. I know everyone is against the Thalmor and would like to see a TES world without them, but maybe we'll see them fall in the next few games.