I'm playing through Skyrim again and I've can't help but think about this question. Regardless of the winner, it suits the Thalmor and the victor has half of Skyrim's animosity (not to mention we kill the Emperor in the Dark Brotherhood quest line). My question is this:

What do you think would be the most interesting chain of events between Skyrim and TES6?

YMMV on how much it actually suits the Thalmor. The only desirable outcome they have is perpetual conflict there ad nausem, and the Nord's are usually quick to reconcile their differences (Nordic civil wars are always notoriously disastrous, but are fairly quick to bury the hatchet) when something worse gives them a cause to ditch what it is they're doing. Given that remnants of both factions continue to exist despite whoever actually wins the Civil War, it effectively doesn't matter. You could paint it so that the Legion invades Skyrim in earnest in a attempt to take it back (however moronic that might be) from the Stormcloaks, or Skyrim's legions are called down to Cyrodiil due to the power vacuum Mede's death leaves the country, setting the stage for the Stormcloaks to regroup and take control.

Given the precedent the series has gone with so far, my money is on the Empire finally fizzling out no matter what. I don't think it will be by the Dominion's hand mind you depending on when the next game takes place, but I'm guessing they'll be effectively defunct given that the Empire has very little control in the rest of Tamriel.