Not to nitpick, but couldn't it be before TWW but after the flood?
No, because the land is closer together in FPTRRL then it is in TWW. Also civilization has actually started.
That's a pretty good point. So, if the Deku Tree's plan has succeeded in linking the land that closely together, then it has to be... what, several hundred years after the Wind Waker? The point is, it would be after ST, which is only a century after PH (right?). Even though he's a magical being and Ganon's evil is no longer thwarting his plans, that's still a LOT of water for the Deku Tree to pave over (a process I've never really understood; is he making the roots of the plants grow together so thickly that they can act as a stable flooring?).
Alternatively, couldn't FPTRR be in the future of the CT, after all the games that feature Death Mountain? While the flood is a good reason for Death Mountain to have a new name, what with the loss of knowledge from past civilization, that point is negated by the fact that the locals actually know what it used to be called. This would imply that the name changed as a simple matter of cultural progression, and that could apply to either timeline. As for the geography... well, after FSA, I stopped putting too much stock in the geography unless there's really no other form of evidence.
Edited by eruntalon, 14 March 2010 - 01:33 AM.