Realistically, the Imperials will have a better long-run chance against the Thalmor... but the story writers will have to be fair and not make come to pass what would realistically happen if the Stormcloaks win: namely... the now alone Skyrim gets ROFLSTOMP'd by the full brunt of the Thalmor's army (instead of spread thin all over Tamriel like during the Great War) and the Empire's back is broken by Skyrim's secession thus leaving the Thalmor unopposed.
I don't see this happening. Ulfric says he worries the Thalmor will invade Skyrim, but with their harsh terrain and the distance, I think it more likely the Dominion would try to finish Cyrodiil off first. Then they could attack Skyrim from fertile lands to the south, with resupply routes across friendly territory. If they do try to invade Skyrim first, IMO it would be because their first goal is to eradicate Talos from the mythic and the chance to accomplish that would tip the scales to outweigh the territorial disadvantages. And then it should be clear that the White-Gold Concordat was the worst thing the empire could have done to their own cause.
Both Skyrim and Cyrodiil are still going to have to work together, even if Skyrim is independent. They'll have to learn to be allies rather than in a one-up one-down relationship.
And if someone can explain to me how being united with the empire helped Valenwood, Elsweyr, Morrowind or Hammerfell against the Thalmor, then I'll buy the argument that being in the empire gives Skyrim an advantage against them. At least one that outweighs the disadvantage of having their blood and mineral resources drained for the milk drinkers in the Imperial City, the enemy invited to prowl their territory and scout at will, and their divine protector weakened.