The timeline is pretty dumb and patchy. A lot of it is really half-assed ("Oh, fuck, we need another timeline. Just say that Link failed in OoT, I guess, and that's it's own timeline or something. Fuck, I didn't know there'd be writing involved in this job!") and it really doesn't add anything to the games anyway. Bleh.
Besides, I much prefer the explanation that the "Legend" of Zelda is retold constantly throughout Hyrule, and each game (barring the direct sequels) is just another version of that same legend.