my gut instinct is to say it doesn't belong in the storyline, but since its incredibly easy to fit in the storyline, I'll let OoX stay.

I think the most awesome way to place OoX (and the only reason I'm placing it) is that each one of the games happens on a different timeline. Both the games start the exact same way (except one is blue and the other is red, note CT Links' shields are blue and AT Links' shields are red) with Link on horse looking down on hyrule castle, and both Link's go and see the triforce, except the triforce sends each Link on a different journey.

And then the ending of the game, where Link stops Ganon from being ressurected and saves Zelda, could be shared by both timelines