Well, I think it's possible that there are two timelines.
(SPOILER)Obviously, in the Windwaker, it speaks as though there was a Hero of Time who stopped Ganondorf. But, since Zelda sent Link back in time, that should have changed time, so that there would be no need for a Hero of Time, Ganondorf would never have Hyrule to himself for 7 years, etc.. And in Majora's Mask, it implies that he didn't go back to Hyrule to grow up to be the Hero of Time. But perhaps he found a way to get out of Termina and back into Hyrule, and then for reasons un-beknowest to me, decides to grow up to be the Hero of Time. Though, we're going to have to wait for an official announcement before we just state for a fact that there are two timelines. There might be another way the games can connect that we don't know about.