The Thalmor aren't some godlike fighting force, they were kicked out of Hammerfell. Sure Hammerfell has the best warriors out there, but Hammerfell isn't part of the Empire anymore and could certainly help Skyrim. The Empire is weak and falling apart, keeping it together might make matters worse for Skyrim or increase the odds.
More importantly however, how would the Thalmor go about invading Skyrim? Send a large fleet, sail past Hammerfell, High Rock then Hammerfell again to land somewhere on the coast of Skyrim? The Nords would have entire armies at the ready for such a situation and it's not like a Thalmor army can march through land... So really, Ulfric does not present a hopeless cause. In fact should he choose not to take the fight to the Thalmor and not to help the Empire in the inevitable second great war he might just offer the Nord longer peace then anybody else.
The conclusions you're drawing do not seem particularly accurate to me. The Thalmor were not "kicked out" of Hammerfell, they simply couldn't afford to invest the troops necessary to beat the snot out of Hammerfell. If they had then they'd leave Valenwood and Elsweyr pretty open and they'd present a great shot for the Legion to circle around the main Thalmor invasion force, isolate it, and utterly destroy it. It would be Red Ring v2, and this time it probably would leave the Thalmor pretty low on troops. It could shift the entire balance and of course the Thalmor know better than that.
As for how the Thalmor would invade Skyrim, the answer is pretty simple. They'd take their sweet time and first take out the other countries of men. If Ulfric wins then the Empire is really just High Rock and Cyrodiil, and there'd be no land border between them since both Hammerfell and Skyrim are officially independent. Thus both High Rock and Cyrodiil would be hugely vulnerable. What this means is that the Thalmor would undoubtfully end up in a position to sack the crap out of Cyrodiil and once that's done, the Empire is gone. Then they'd move on to Hammerfell, then they'd take High Rock, and then finally they'd do a three-ponged land-based invasion of Skyrim. It might not happen within Ulfric's time, it might not happen within the next 100 years, but it would happen eventually. Time would be working for the Thalmor.
That being said, you're quite right that the Thalmor don't have a god-like army. In fact their army isn't hugely impressive in open combat and it's not huge either. It's simply large enough to get things done. Their real strength is in espionage, covert operations, and manipulating every fight to be on their terms or not at all. Take that away and they lose their potency. Let them play their divide and conquer games and they'll win. I shouldn't have to say that Skyrim alone obviously isn't stronger than Skyrim + High Rock + Cyrodiil. And once open war against the Thalmor breaks out again, I'm sure Hammerfell will come back into the Empire as well.
A Bosmer who sides with the Empire? It's possible, but you'll be considered a rebel in your homeland. Valenwood is Thalmor territory. If you imagine yourself a resistance fighter against the Dominion then perhaps you could role play that. But the implication is that your family and loved ones back home would probably suffer horribly for your actions.
Valenwood is Thalmor territory but not because the Bosmer love the Thalmor. Most Bosmer are borderline pacifists and would rather surrender than fight an all out war, which is quite contrary of what the Thalmor believes in. The Bosmer don't care too much who claims to "own" their land as long as they get to live there in harmony with their trees and the forest isn't cut down. What you shouldn't forget is that the Thalmor are very brutal and have a certain fondness of purging their political opposition, which means a lot of Bosmer are brutally oppressed or executed. Fighting the Thalmor is not "treachery" to other Bosmer, it's merely not peaceful tree-hugging.
The same thing applies to Khajiits, by the way. Khajiit don't care about titles or rulers, they care about their home clan and about living how they want to live and using moonsugar and skooma as much as they want. They aren't loyal subjects as a race, even if a few might be overly religious and thus bow to the Thalmor on that
accord.
Skyrim is the land of the Nords, and the Empire's presence threatens their way of life and their beliefs. Not only that, but the Empire is now just a puppet for the Thalmor, who aim to control and eventually destroy that which is not Thalmor.
This is not exactly true. And Tulius says something that hints to this as well, even if his position prevents him from making any statements of open aggression against the Thalmor, since there's officially a peace treaty in effect. The Empire is by no means a puppet for the Thalmor. More accurately, there's a cold war going on but the Thalmor have all the trump cards currently, which means a direct confrontation would be unfortunate.
While the Legion could in theory destroy any army the Thalmor could put in front of it, the trouble lies in getting the Thalmor to actually fight a decisive battle. The Thalmor know their limitations just as well as the Empire does, which means they'd to Al Queda style terrorism and small hit and runs all over the place. And with control over both Elsweyr and Valenwood, there's a huge border from which they can stage their attacks. The Legion can fend off those attacks if it can make it in time, but going offensive against them involves invading both Elsweyr and Valenwood, and sweeping both provinces clean of all the Thalmor guerilia groups. That's not easy at all. Even then, the Thalmor home province would still be intact and unharmed while the Empire would be worn down.
Ulfric's approach seems to be "fight until you die and never surrender!!!" and while that's both brave and admireable, it's not always the most intelligent choice. Fighting makes sense when there's a victory condition to be achieved, but if no paths lead to the achievement of victory conditions then what exactly is the point of fighting? Consequently the Empire is swallowing its pride, licking the Thalmor boots, and waiting for a time when hurting those pointy-eared bastards is actually possible.
By the way, a man Ulfric would've benefitted a lot from knowing: http://en.wikipedia.org/wiki/Pyrrhus_of_Epirus