One thing that has been nagging me is how Bethesda will integrate Skyrim's Civil War, in which you can lead either side to victory, into the lore for future games.

Obviously, only one side can truly win the war. And yet in-game you hae the option of leading both sides to victory with different characters.

Who then, do you think Bethesda will decide wins the war for real? And how will they integrate that with the reality of the game, which is that many people will have experienced the opposite side winning? Will they say something like "Legion/Stormcloaks were defeated by one known as the 'Dragonborn', but fought back after s/he mysteriously vanished to reclaim victory"? Or will they say that the outcome has been lost to history, even though such an explanation would require an almost apocalyptic catastrophe to be at all convincing?

I think in keeping with the general trend of the Empire falling apart, the Stormcloaks may win the war in the lore. But that is pure speculation, and I have no idea what Bethesda are planning. How do you see it?

I don't think it will be resolved in a manner that says that either side wins, just like the ending of Daggerfall wasn't erstricted by the choice you made since every and none of the options happened at once.
My guess is that there will be some vague references to the war and that it was supposedly ended, but that the victor have been lost to history and that the Dragonborn was involved somehow. Or we might get two opposing sources, both claiming that one of the sides won.

Vagueness is one of the lore's best tools. "The Civil War in Skyrim? Such a blood conflict." It's mentioned, but not in immense detail so the outcome is never truly revealed. It might also be overshadowed as a minor conflict in a Second Great War with the Thalmor, so nobody ever really cares to mention the outcome.