Normally, everything happens in a TES game. So, in Oblivion, the Champion became Listener, Gray Fox, Champion was of all races etc etc to get a decent story in the next game for every player. I expect this to happen for Skyrim too, so that in TES VI the Dragonborn would have been Harbinger , Listener etc. But now we have conflicting questlines, the Imperial Legion and the Stormcloaks, as they obviously cannot win both. So, what do you guys think that will happen. Will we hear in the next TES game that he wasn't involved in politics(what I expect), or did he choose a side?

Nobody remembers who won the Civil War - Second War with Thalmor started soon after the Civil War was over and so the memory of victory was lost during Great War II where the whole mankind fought for their right to exist. That's what I suppose to happen.

stormcloaks won then were over-run by the empire or vice-versa. it is the only way the could both win

But that would influence Great War 2.0, as it would be the Empire vs. the AD, or Skyrim vs. the AD.

Wow that makes sense , I was breaking my head thinking of a reason for this..

I always assumed that the "official" story would follow the truce that is eventually made in the main quest if you haven't picked a side in the Civil War.

From there, probably some sort of Thalmor invasion.