Since even he's not sure where it fits, and from what they say, they keep the timeline reserved in their secret Nintendo clubhouse, I'm gonna call an ass-pull on these. =P Maybe Miyamoto had the vision of a Zelda game before all the others in OOT (although he said this new Skyward Sword game was before OOT), but he certainly didn't campaign it. We were never told about the timeline directly, never told how we should look at them, except one thing that fits in EVERY. SINGLE. INTERVIEW. That they always develop every single Zelda game as a whole new world and experience, worrying more about gameplay, and just keeping the main elements of the game alive.
Miyamoto isn't Grant Morrison. He doesn't set up huge stories through years so we can follow small details of them through convulted timelines that may or may not relate to each other. The dude makes games. For gaming. And in each game, he makes a whole new experience. I've yet to see a game from him which was actually a "sequel" to anything story-wise, instead of a whole new thing.