RIP Nintendo Power

[Mutsukki]

The concept of reincarnation, which is a normal one in Japanese culture, is what's in play here. I mean, since Wind Waker it was obvious (for me) that they were not the same person at all, but rather reincarnations. I'm pretty sure the game tells you that in big bold letters even (Tetra turning into Zelda, King of Hyrule telling his history, the opening cutscene. And look, Spirit Train actually puts you in a kinda close timeline to Wind Waker, but with another Link), I never thought that was confusing. The timeline surely is, but not that particular concept that every Link and Zelda was a different one.

Also, about Ganon(dorf), he's the only one that I'm kinda sure is the same person on all games (even the ones he's a pig), since he's supposedly ridiculously old, immortal and always break the Dark World seal.