I would say that Wind Waker came first, in 2000 spaceworld they were demonstrating a Zelda engine with awesome graphics, which they said they used instead with the WW graphics, so the WW engine itself has been in development since the late 1990s, since the first WW screenshots came soon after you can only presume they were toying with those graphics before spaceworld as well.
Since the gameboy advance was not released until mid 2001, and the Zelda wasnt released until 2003, and the Wind Waker was released in 2003. I'm guessing a 3D game you dont have an engine for might take a lot longer than a GBA game you already have a full engine for (the LTTP engine). Based on this, the WW style definitely came first.
But as others said, thats the obvious answer too.