So the civil war questline in Skyrim ends with either the Imperials winning or the Stormcloaks winning. This decision is ultimately decided by the player when choosing sides at the beginning of the game. My question is: how does Bethesda decide what happens next in the series if the ending of Skyrim (aside from the Dragonborm main questline) was left up to the player? OR did they just decide that the Stormcloaks are supposed to be the victors (cannon)? Does that make sense?

I think they'll probably end up having something happen between Skyrim and the next game that renders the outcome of the civil war largely unimportant to whatever province the next one takes place in.

One of the other topics here went off on a tangent regarding the matter. But either way, Ulfric and Tullius will both be gone by the time the next game happens. As for what that entails, the precedent throughout the games is for the empire to continue rolling downhill, so whether or not that'll hold true here remains to be seen.

I expect Mede's assassination will have a impact on Cyrodiil (And that it'll happen no matter what), because drama.