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Legion vs Stormcloak is one of those topics that starts heated threadnaughts. But just consider that the Stormcloaks are really quite racist (Dunmer ghetto, Argonians not allowed inside) and while Ulfric makes nice speeches, ultimately Ulfric only cares about Ulfric - he's in it for the power grab, not for independence or religious freedom. Siding with him is not much different from siding with Hitler. Morally, if you side with the Legion, Talos worship may remain outlawed for a while longer, but you have a better position from which to destroy the Dominion later on. The Nords are not the only ones worshipping Talos, you can be sure that the rest of the Empire wants out of that situation also. And noone in the Legion enjoys licking Thalmor boots, they are certainly not willing allies.
Mechanics wise, all that really changes is that a couple of Jarls will get replaced and some cities will have different city guards. They still offer the same quests as far as I saw. Also, if you resolve the rebellion before finishing the main story line, you will miss out on one of the best (or worst, depending on who you ask) story events in the game, the ceasefire conference.
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