I hope Stormcloack but who knows I'm sure they will find a way to cop out and appease both sides.
Thats the thing, this is a really difficult cop out. Go to UESP, go to the lore page, it is really detailed, I mean, really detailed. Game of thrones/Lord of the rings history detailed. If they provided only a general overview of world history, and TES VI was 500 years from now, yeah, they could ignore that, but the history of Tamriel is too well recorded to just forget about a Civil War.
The only cop out I could think of is that in a DLC, Thalmor invade, they destroy imperials/stormcloaks but are ultimatly repelled. That way, they could say that the victors of the Civil war were victorious for such a short period of time that it is difficult to know who won.