I think the Empire is best. Think about it the Thalmor lived quietly and let the Empire be the number one guys on Tamriel, while they slowly and carefully chipped away at them, the Empire needs to do the same, keep Skyrim and wait, they will grow stronger and at the same time slowly try to weaken the thalmor until they can beat them in a war then they'll make their strike. The key is patience, the thalmor didn't just revolt and then invade Cyrodiil like the stormcloaks want to (except they'll invade Alinor) they just sat back and watch the empire crumble.
Not really. The Thalmor wanted no side to win, only to have a long and brutal civil war that drained both badly.
An independent Skyrim would mean one less country the Thalmor are allowed to operate in, and it allows Talos to stay in effect. Not to mention, an invasion against Skyrim would be awful. It's a cold, mountainous, and dangerous land, not a flat bowl (Cyrodiil) or a tropical paradise (Summerset). A victory for the empire would mean it still stands with a still capable fighting force.
Also, the empire seems to be doing NOTHING against the Thalmor. Then again, no one can really enter Alinor, unless they are Thalmor, and no human would be allowed to be Thalmor. The only thing anyone can do against the Thalmor, would be to, somehow, get plants in Valenwood and the two states of Elswyr. Even then, nothing against Summerset directly.