Here is the "What If" as I see it
After the Civil War, now that Skyrim is weakened, no matter what side would win, the Thalmor are in a great position.
I would like to see the Thalmor planning to invade/take over Skyrim. All of the sudden, Solitude would be Lost, under Thalmor full control. The access to the sea will allow them to bring more force in.
After Markrath falls under their control, the people of skyrim start to realize what is happening. The Jarl of Whiterun will start the resistance.
You will have to choose side: Helping the Thalmor or Defend Skyrim
Intrigue and negotiation will be the name of the game at the start, to avoid/help the Thalmor to spread.
How much money will be needed to keep/take Riften with the TG agreement? How much also to keep Falkreath, we will have to see with the DB. The last Quest of the DB can also brings you to a twist, learning that Amund Motierre actually works for the Thalmor. Both way, you will have to kill the emporor, but you will learn that the Thalmor promised Motierre to be the regent of Skyrim, when they would have full control of it.
You will have some epic battle to Take/defend Markarth, Solitude, Whiterun or Windhelm. You would be the lead general on your side...