I think Nintendo sort of rushed it with their timeline for Zelda, as you can see, over the years, the games have developed higher, and more advanced technology.
But actually, the order in which the games were released in, is completely different, take
SS for example, it is the most technologically advanced, but yet, it is stated the first Zelda game, but it has Grapple-Claws you control with some... I don't even know, and all the 3D Zelda's have featured some sort of throw-and-pull kind of thing, which is futuristic! We don't have that yet.
So my theory behind this, is that Nintendo will release a new timeline, along the release of the next (Wii U) Zelda game.