This goes back to something I've been saying for awhile (and something which annoys a lot of Zelda fanatics...)... basically, there is no time line.
I truly believe that Nintendo (i.e.: Miyamoto and Co.) have a basic idea of how the games fit together - but it would never hold up to scrutiny, as there's no way to piece the games together without issues coming up (like trying to piece the Oracle games between LttP and LA, which everyone friggin' tries to do). Additionally, it's only the time line until the next game comes out, which could effect how the "official" time line fits and works together.
Basically, Nintendo isn't going to let the idea of a "timeline" get in the way of making a good game - and the story told in that game is always going to play a second fiddle to the game play. If someone comes up with a great idea, but it doesn't fit into the story line, they're going to shoe-horn it in.
i.e.: the timeline only exists until it's changed again.