No matter how you play the civil war, you help the Thalmor.
If you help the Empire....well it gives them free reign through Skyrim as if nothing happened.
If you help the Stormcloaks, it makes the Empire lose one of it's strongest allies softening them up for the next invasion.
Would be nice if we could actually undo some of the Thalmor plans a bit....but they are just so prepared for everything.
Actually, according to the Thalmor themselves, perpetuating the civil war into a stalemate is their optimal plan.
If the Imperials win, they can go back to recuperating their strength from the first Great War, meaning that they'll pose a greater threat when the Thalmor attempt to finish the job. The Thalmor got hammered from the Great War too.
If the Stormcloaks win, there is a new nation openly hostile to them
now who is openly worshipping Talos, and now their own recuperation is interrupted by having to (attempt to) put down this new nation.
The Talos worship ban wasn't just because the thought of a man undergoing apotheosis is offensive to them... Talos is what is holding the Mundus together. He is the hub in the wheel. Take him out, and the Thalmor's plan for unmaking the Mundus and erasing all of men from reality and returning to pre-creation "divinity" succeeds. And how do you kill a god? You quash belief in him.