While it would be epic to suddenly get a timeline which made perfect sense someday, I don't think that would be possible. The way I see it, The Legend of Zelda is like Wheel of Time. For those who haven't read those books:
Time is like a wheel, with seven spokes in the WoT, and each spoke is an age. Let's say that the first LoZ happened in age four. Each age is at least a couple of thousand years, and I guess they can be hella longer. So when age five comes around, the stories are still told of Link. In age six, things are getting murky. Did it really happen? When age four comes along yet again, the stories from the last time is but legends. Mostly forgotten, and all that is really remembered is a hero in green clothes.
Link is reincarnated each time this age comes, to battle Ganon. He is like The Dark One, someone who needs to be stopped by the forces of good. Of course, this doesn't really work, since it is not always Ganon who is the enemy. But things change with each turn of the Wheel, so why not?
I think this is the best way to explain it really. If it was all just a retelling of one legend, things wouldn't change so dramatically as they have. But if this is the same event, just in a different time, then it could work. This is going to be my view on it till they actually reveal a timeline, which I am sure they will someday anyway.