It's true that most quests before only had one way to go or weren't important enough to be acknowledged decades or hundreds of years later. But in Skyrim, the decision between siding with the Imperials or Stormcloaks, or not getting involved at all, seems like it would have a major impact on the future of the land, if not all of Tamriel itself.
Stormcloak winning could inspire the other provinces to rise up and declare their independence from the Empire.
Empire winning could further strengthen the Thalmor's hold on Tamriel and lead the races 'lesser' than the elves to slavery and persecution.
And not doing anything could make the result go either way.