I honestly don't see why everone cares about the time line. I don't think shigsy ever intended all the games to fit togather on one grand scale. We should really just try to look at the games as individualls, only then will we not get distracted by decades of story that have nothing to do with THIS GAME anyway.
I don't see zelda games as being on one timeline but more basic than that. Bad guy kidnaps zelda, hero of time comes around... claims master sword, saves zelda and in turn the world by slaughtering evil. Its classic.
Simple as that.