I think folks are using sleeper agent and asset synonymously, which is what is breeding confusion. Or, they read the word dormant in the dossier, and assumed it meant sleeper.
And yet they somehow miss the immediately following paragraph, in which it is stated that he wants nothing whatsoever to do with them. Furthermore, Ulfric himself, if you actually listen to what he says instead of dismissing it out of hand, goes on at some length about how he despises them. Between these, I've no idea where folks are getting the notion he's a Thalmor agent.
As to which group is better-equipped to fight the Thalmor: the Empire is in a much better position to do so geographically, however they aren't really showing the will for it. Conversely: the Stormcloaks most definitely have the will for it, but cannot reach them unless they first take over Cyrodiil (I don't see an alliance between the two happening any time soon, if ever). While I typically stay out of the whole Civil War mess, as in the long run both sides are going to lose in some fashion, in the bigger picture I'd honestly have to go with the Stormcloaks because the Empire has destrroyed pretty much any and all possibilities of getting future alliances with the other provinces after their behavior towards Hammerfell. Whether or not the Stormcloaks can arrange such alliances still remains to be seen, of course, but I'm pretty sure they'll have a better chance of it since they won't have the albatross of betrayal perched on their shoulders during negotiations.