Joystiq just finished featuring a series of GameTrailers.com videos on The Legend of Zelda franchise. There are links to the other parts on Part Six's Page (I would link to the GameTrailers.com site, but the site sucks). Part six is separate to all the other parts so there is no spoilers in viewing Part Six first. And yes Part Six it solely concerns itself with The Legend of Zelda timeline as suggested by this post's subject line.
The proposed timeline sounds like it makes sense (not that I have ever played a Zelda game from start to finish), but Oracle of Seasons and Oracle of Ages released on the GameBoy in 2001 where originally going to be representative of the Triforce and be three games, not just two.
I don't think Miyamoto has a grand scheme for all of this so I don't think any of this matters. What everybody should do is start asking real questions like, why does Twilight Princess still have MIDI music and why hasn't Nintendo moved to replacing the tedious text with voice acting!?