I'd like to see these take place on summerset isle... The only issue i see here is being able to streamline both the Empire and Stormcloak factions to have the same quests and ending.
They could always make it like i said, The StormCloaks may be resilent, and angry... but there resources are poor, and there man power even worse... they stand no match against the Aldemeri Dominion. The Empire on the other hand does... so a treaty is struck up, the Nords get to keep Skyrim, as long as they work directly with the Empire in fighting of the Aldemeri Dominon, and then the Empire later uses Skyrim like a Protecterate. The Empire rules over Skyrim, and will protect it, but Skyrim is free to have its own Government and Religions.
Also another idea that just came to mind, that can easily be worded in the history books so it could fall either way... what happens... is...
Second Great War breaks out
With the help of Dovahkiin the Empire wins
Empire destroys the White-Gold Concordinate, and Talos resums being praised all over Tamriel.
Thalmor are pushed out of Skyrim, and back to Summerset Isles.
The Empire goes into a Golden Age due to the harsh punishments they put on the Thalmor.
Skyrim rejoins the Empire, no longer angered by the Empires weakness, and Talos being banned.
All that is mentioned in the History books is the Civil War, then the Great War that broke out before the whole Civil War conflict could be resolved (Honestly it isnt all resolved by the time the quest line ends.)
Boom there you have it.