Many-worlds interpretation of quantum mechanics implies that all possible alternative histories and futures are real, each representing an actual "world" (or "universe"). So, way I see it, these 3 Zelda timelines are just what Nintendo decided to present to us (so far).
BTW, for those interested in bit more info:
http://zeldawiki.org/Zelda_Timeline
And all props to GT, things like this are why I like them so much (Invisible Walls being main reason, of course).







