I've always thought that PH would take place in the area that AoL took place in (albeit flooded). Even before the game came out. Even while it was just being called "Wind Waker 2" . . .
It's just something I thought they'd finally get around to. But when actually playing the game and encountering Maze Island (in roughly the right place it should be in) . . . . that confirmed it for me.
I'd love to see another game take place in this landscape. It's vast and interesting and ripe with potential.