Please correct me if I'm incorrect about any of this lore.
I hate the Thalmer as much as the next guy, and believe me when I read that dossier I was pissed. But when I stopped to think about it, the Empire gave up without even trying to unite all of Tamriel and keep fighting. The Thalmer are in a weakened position as well, that's why there was a treaty and not a full hostile takeover. I sided with the the only guy that had enough balls to kick some yellow elf ass, and that's exactely what Skyrim needs or it's going to get stomped.
Throughout (our) history people protecting their own homes with gorilla tactics have protected their homes against far more powerful enemies. With the mountainous terrain and ferocious wildlife of Skyrim, and complete takeover would be near impossible. Remember these people are fighting for their faith, the most powerful motivation there is.
Half the empires army is Nordic, and all true sons of Skyrim would gladly fight to protect their homeland. Not to mention that the army of Skyrim is led my the Dovahkiin and his dragon army!!!
The Dovahkiin has one dragon sworn to fight along side him, and Parthurnaxx which leads half of the remaining dragons! These dragons are very smart, and would be willing to unload their urge to slaughter for the only man that can easily kill them for good.
If the Thalmer are the bad guys, and the Empire is wrong, what does that make me? It makes me right!