Apparently we were all a little too excited when it came to the Legend of Zelda timeline, released in Hyrule Historia last month. I say that because instead of being sensible and reading the book in order, people who received the book early just jumped to the timeline and put it up on the internet. They should have read a little disclaimer written by Eiji Aonuma that says "the story is just tacked together after we've focussed on the gameplay and probably shouldn't be taken too seriously," then none of us would feel the egg on our face.
"Chapter 2, "The Full History of Hyrule," arranges the series in chronological order so it's easier to understand, but from the very beginning, Zelda games have been developed with the top priority of focusing on the game mechanics rather than the story. For example, in Ocarina of Time, the first installment of the series I was involved in, the main theme was how to create a game with pleasant controls in a 3D world. Or in the DS game, Phantom Hourglass, the focus was having comfortable stylus controls. Finally, in the most recent game, Skyward Sword, we focused on an easy way to swing the sword using the Wii motion plus.
Thinking of that way of developing the games, it may be correct to say that the story is an appendix to that. I even think that setting Skyward Sword as the "first story," was merely a coincidence.
While reading over "The Full History of Hyrule," it's possible that some parts may look contradictory. For instance, the Mogma race or the beetle item that appear on the very first story do not appear on any other game that takes place in the future. I'd like to ask everyone just to enjoy the book and to be broad-minded, and to think that those parts are the way they are because of the way Zelda games are developed."
So, basically, the super secret Nintendo-only timeline that has been guarded by mythical animals and Roman guards since the late eighties is non-existent and overthinking is a bad idea – thanks Nintendo!
If you'd like to read the rest of the book, you can check out the translation project at GlitterBerri.
