In regards to the OP, my opinion is simple. You need only make two decisions : 1st : Do you think the current empire will eventually (after rebuilding strength of course) re-start the war with the Thalmor? If your answer is NO, you must side with Storm Cloaks. If your answer is YES, you have a second decision : Which force is most likely to defeat the Aldmeri Domion ? Empire without Nord assistance or Empire with Nord Assistance? If you choose the former, then it just comes down to whether you personally like Stormcloaks or Legion best. If you choose the latter however, you MUST choose Empire. To do otherwise is unwise for any sane Thalmor hater, no matter how you slice it. Occams Razor, as ever, is sharp.
This is what i agree with. The Empire may be battered, but its hardly out, and there is a huge wealth of information presented in game that suggests they plan on picking up where they left off, once they are sure they can win.
Of course, it all boils down to whether or not you beleive the statements made by Tullius, Rikke, random Legionaires and even the Thalmor.
Similarly, you ahve to put a degree of faith in Ulfric's statements that he wants to drive the Thalmor out. Without knowing HOW either side will play out, its all a matter of faith.
The Empire also already has a history of dissinformation with the Thalmor, to the point where they have been able to catch the Domminion completely offguard and wipe out the bulk of their armies. As such, i don't view the Thalmor agents within Imperial lands as a threat to the Empire's security beyond the fact they rile up the peasents.
Contrary to the arguement that Hammerfell beat the Thalmor, it was Empire Legionaries (Dismissed as a way to circumvent orders) which held the line, and they faced a crippelingly depleated Aldmeri Domminion during that post Great War conflict.
Now, in my mind it boils down to who stands the best chance of stopping the Thalmor. That's the Empire, under the asumption that the Empire DOES take the fight to them again. I know there is a push with this game to love the province of Skyrim, but as far as i'm concerned, the Dragons can have it if it means Tamriel is a safer, Thalmor free place. Damn Skyrim and damn the Nords, Tamriel comes first, and the Empire has the best chance of keeping it safe.
What we really need now is a Breton warlord who can trick a powerful Draugr into fighting for him... Oh, i'm sorry... Right... Talos came from Atmora...