As for the war itself, I think the Empire will somehow win. They are the child of Bethesda and have ruled Tamriel in all of their games (minus Skyrim). Skyrim was necessary to show that the Empire isn't infallible, but I think they will bring it back in strength.
Even if the Stormcloaks win the war, a dedicated Thalmor attack into the Empire or Hammerfell might prompt the Stormcloaks to come to their aid. Afterall, the Stormcloaks HATE the Thalmor and they know just as well as anyone else that if the Empire or Hammerfell falls, they'd be close on the list of next ones to go, due to worshipping Talos and all.
IMO Hammerfell and Skyrim will be reconciled with the Empire during the Second Great War, victory will be achieved, and Skyrim/Hammerfell will fall back into the Empire. Perhaps a Nord Emperor will sit in White-Gold Tower as part of the deal, and pro-Empire ideals and Talos worship will once again become prevalent.
The only way I can see a TES game involving a player-character in the Thalmor's downfall is if the war ends in Imperial victory and the Thalmor become a renegade group like the Mythic Dawn that maraud around Tamriel attempting to blow up Towers, and its up to the PC to save the towers and strike the Thalmor base or something. As far as fighting the Thalmor while they are the head of the Dominion, that just doesn't fit TES' vibe. You wouldn't be interested in exploring and doing side-quests if you were fighting a full-blown war with the Aldmeri Dominion.
I could be completely wrong of course, and perhaps Tamriel will fall under a new empire for the first time in history. Perhaps all of Tamriel will be the Aldmeri Dominion lol.
EDIT: When looking at a map of Tamriel, Summerset Isles, Valenwood, and Elsweyr combined are barely a bit largely than Cyrodiil. Its possible Beth won't release a new game for awhile and we'll get all three provinces shipped in one game. Or maybe just Valenwood/Elsweyr, or something, because those two provinces combined don't even equal to Cyrodiil's size.