The Zelda games span many millennia, following the history of Hyrule. At the center of each game are two characters: Princess Zelda and Link. These characters are not meant to be the same people throughout time, but rather different players filling certain roles throughout time.
When Hyrule is in need of a hero, a hero presents himself.
The Wind Waker makes it very clear that its Link bears no relation to the Hero of Time (the Link from Ocarina of Time), but goes out of its way to explain why he’s dressed the same. In Ocarina of Time, Link’s wears a green tunic because that’s what all the people in Kokiri Village wear. In The Wind Waker, Link’s village makes every boy on their birthday dress like the Ocarina of Time Link. It’s flimsy, but it’s cute and it accomplishes two goals:
- Functionally, it gets Link in the traditional outfit.
- Story-wise, it establishes that The Wind Waker is a legacy entry in the series. The history of what came before in Hyrule is important to its characters and its world.
Later games in the Zelda timeline do not make such strong attempts to explain why its Link is always clad in green.
There are also other characters sharing names and roles throughout time. Gravediggers are always named Dampe. Zelda’s handmaiden/bodyguard is always named Impa.
But that rule does not translate to all characters. The Wind Waker’s Link and Zelda are new players filling out their pre-destined roles, but Ganon/Ganondorf is the same person.
This is a small nuance I appreciate. In The Wind Waker, Ganon sees and understands the prophecy of the Hero of Time returning, aided by a Princess Zelda. The Wind Waker’s entire plot is based around Ganon attempting to stop that prophecy from coming together. He is kidnapping young blond girls, because he wants to find and stop the new Princess Zelda.
And oppositely, Zelda and Link are players in a plot they do not understand. Link’s call to action is rescuing his sister. He has no idea that his sister was kidnapped because Ganon is trying to find and kill Princess Zelda. And Zelda has no idea who she is either. She’s just a pirate roaming the seas.
Ganon and the King of Hyrule are the only characters who know everyone’s role in this particular legend of Zelda.
 Some games take place outside of Hyrule and do not feature Princess Zelda (Link’s Awakening, Majora’s Mask, Oracle of Seasons, Oracle of Ages). Generally, these games follow a Link after he has saved Hyrule and set out for other adventures. For example, Majora’s Mask’s Link is the same as the Link in Ocarina of Time.
 The King of Hyrule refers to him as Ganon, while Ganon/Ganondorf refers to himself as Ganondorf. Chronologically, The Wind Waker takes place after Ganondorf has transformed into Ganon at the end of Ocarina of Time, but I find it interesting that Ganon still thinks of himself as Ganondorf.