The Thalmor don't run the empire. Concordat's purpose wasn't so they could control the empire but rather so they could maintain a presence within the empire for intelligence and sabotage. And it's doing just that, they've delayed the Legion's rebuilding efforts when they demanded the Talos ban be enforced in Skyrim after the Markarth incident, thereby triggering the civil war.
I don't actually think the Thalmor are that strong from a military standpoint. Hammerfell is a clear example of that (even if Redguards are regarded as the best fighters in Tamriel). At the same time, I don't think the Empire will completely collapse. The imperials, as their name suggests, I believe will always have some kind of Empire, but it definitely won't be to the same magnitute as it was in the beginning of the 3rd Era - and I think that's a good thing for the sake of variety. *SPOILER ALERT* The DB questline loosely implies the Elder Council are actively seeking to replace the current Emperor. Nonetheless I don't think the Empire will regain its strength without some inspiring figure like a Dragonborn (unless Beth decides to skip another 200 years and write that the Last Dragonborn's descendents took the Imperial throne).
Alinor is a huge mystery. But I get a sense the Thalmor takeover was a bloody one. I have no evidence for this, just a feeling. Also one of the Imperial Legates makes reference to ethnic cleansing of various woodelves in Valenwood? I'd be surprised if there wasn't some resistence effort brewing up. If the Thalmor are to be defeated, it'll be internally. But I think they're here to stay for a while because an evil dominion is a useful plot device.