I'll start of from a gamewide perspective-
A Thalmor war?! Holy crap! Sweet! But, how do I start it? When? And.... Come to think of it, me and what army? Everybody is busy with a Civil War. And Dragons. Wouldn't I have to finish the Civil war to do this? Geez, those are some big possibilities for it to take in. A story for an Ulfric leadership? Story for an Elisif/Tulius leadership? Shouldn't I deal with the Fire-Breathing winged apocalypse that wants to eat the universe before I take sides in this war?
Think about it, too many variables and to much "when". It makes sense for a war to start, but when? Ulfric could mobilize and go to war immediately, yeah... But he's not even king of his own country, yet. And Tulius might have the resources and orders.... Soon? If the Empire wants to go back to war, sure! But it's hinted that the hold back due to lack of resources. I mean, peace in Skyrim would make it easier, but I don't think things would be peaceful IMMEDIATELY after an Imperial victory... C'mon now. There just isn't really a good moment to set it up, and the story would be awkwardly timed for concurrent questlines. Now, maybe it could be a Lonesome Road deal, where it's an option all the time but only makes sense if you do everything else first. But even then.... That doesn't sound all too sensible. I just can't find any good timing.
Now from Bethesda's perspective-
HOW CAN WE POSSIBLY MAKE SO MUCH WORLD-CHANGING STUFF FOR A GAME THAT IS LESS WORLD-CHANGING THAN THE STUFF?!
A THALMOR WAR. That's a massive undertaking. You'll need out-of-country territory. Lots of it, because battlefields are big. A lot of battlefields, too. Cities to take. Officers to serve and kill. Weapons to use. Spells to cast. Enemies to spawn. This DLC, to be coherent, Needs stuff. SO MUCH STUFF. Even in Skyrim's scaled-down reality (Whiterun? A Major City? HAHA OH WOW), battles of this much canonical magnitude will be HUGE undertakings. I'd guess that a war would probably travel down to mid-Cyridiil, with Imperial City being the southernmost location. End things there, right? That'd a lot of space. I'm probably way off, but that sounds like almost as much territory as Vanilla Skyrim itself! Sheesh! You really expect that out of Bethesda? Maybe around Shivering's time, I would too. But think about how relatively puny DG, DB were... Yeah, half a country isn't happening. There's no way we'll get that much content.
Plus, how can you end it? A war? Obviously you can't end things with a Thalmor victory. But a Thalmor defeat means a lot of change. No more Concordant, Elenwyn and her Justiciars have to leave, we can worship Talos freely... Hey why were the Viking and Roman dudes fighting again? Something about a Boot or Loot or something? Can we go home to our families now?
You just can't end a war with the Thalmor conclusively... Which is exactly what we all WANT. Chase them out of Skyrim, who cares Ulfric was going to do that anyway? Out of Cyrodiil, they had mostly left already anyway. Now, march into Alinor and destroy the Nazi Elves in their home turf? Yes please! That's exactly what we want. But... What next? What happens next? Too many questions, too much to follow. It can't happen in-game. And Beth won't have the guts to disappoint players leaving them hanging on a border between Aldmeri land and Empire land.
Finally, The Geopolitical Climate-
Summerset Isle and Skyrim are far, far apart. This game, and it's story, is about the province of Skyrim. It's about the people of this land, and their lives. It's about it's organizations and deep dark secrets. It's about saving the world from Strangely-Slavic Dragons and magical screaming. The Empire is there, as always. But it is not about the Empire. The Empire isn't the Continuing Story of TES, it's just a longstanding presence. If there is a story to be told about the Cyrodiilic Empire, it will be told in a game about the Cyrodiilic Empire. The dominion will probably fall, but more than likely it will fall in-between games.
Even so, there's too much Marketing to be done with the Thalmor to kill them off so soon. TESO will have a Dominion. I can easily see these becoming a long-term "Big Bad" for the series. They already have an established style- Symetrical, feathery Black/Gold designs with maybe a hint of red in there, and Eagle motiffs all over the place. Too much style to throw away. I'd bet a hundred bucks they'll be as aesthetically established as the Dwemer, Orcs, and Empire by TES VI.