For one their whole meaning they stand behind makes no sense the empire was made by akatosh so therefor skyrim is originally the empirals home. Also during the thalmar embassy mission theres a ledger about ulfric stating that he is working with the thalmar so the rebellion is all just a big ruse from the thalmar to break apart the empire so they can take over more easily. Some of you may know this allready but for those having trouble picking sides hope this helps!
Empire was made by Talos, you may be thinking of the First Empire, and Skyrim is the first place the Nords landed in Skyrim, and the Imperials descend from them. It is not the same Empire anymore, no more Septims. The Thalmor want the civil war to continue, but not to end, but yes, that is what they planned.
But all in all, the Stormcloaks are just as bad/good as the Empire