Hmmm.... Don't you think it's cooler when you're always playing the same Link that encounters the same Zelda?? Because I would, it's just good to think that Link is
one hero and there is only
one princess and that's Zelda (and Peach of course). I don't like the multiple Links and Zeldas theory, it simply doesn't feel right.
So I'd rather have a story that doesn't make much sense, than a story with multiple L's & Z's.
They will never be able to fix the story now. I mean the 7 Sages were Men in ALttP, how can their offspring be Zora, Goron, Kokiri and Hylian?? You can't explain that, not even with the theory.
And Nemesis:
OoT
MM
ALttP
TLoZ
Zelda 2
The gameboy versions come in between OoT and Zelda 2.