I believe they'll have a Thalmor war (or some similar event) take place after the events of Skyrim which will be the main focus of the past. Whether the Empire or the Stormcloaks win would be left to interpretation, chances are the event I'm suggesting would have happened regardless who won the civil war so it wraps up the past in an open enough manner that player can decide to believe what they want without spoiling it for other players.