Well I know most fans have their theories, but I honestly don't think Hyrule is supposed to rise again after Wind Waker.
I just replayed that game and it is made very clear that the land Zelda (Tetra) and Link are going to find will NOT be Hyrule at the king's request and demand, but a new land for the future. Hyrule is dead and buried forever.
Which to me makes all 2D Zelda games besides A Link to the Past and Link's Awakening (which was a dream anyway) very hard to place.
My theory is becoming more and more that there is a different timeline for 3D Zelda games.
First of all I never bought into that alternate timeline BS, I think hippie hunter nailed on the head what I thought of the ending for the last 7 years to Ocarina of Time. After that, Majora's Mask clearly follows. And Wind Waker is clearly the descendants of OOT as that story is the one specified in the opening sequences and when you go down to Hyrule (old Hyrule) besides clues down there of it being the obvious (including the Hero of Time's statue) there is the stained glass windows of the Six Sages from OOT.
Now the gap is when Hyrule was flooded. My guess is Twilight Princess is about the new Link taking place over the old Hero of Time who has passed away (whether with Zelda or not) and his failings to save Hyrule and would thus connect the saga and complete the 3D Zelda world.
Now considering that GAnon was locked away in the Sacred Realm at the end of OOT and he escapes and plunges the world into darkness in A Link to the Past to me that would fit wondedrfully between MM and TP though it would disagree heavily with WW's legend.
And you can tack Link's Awakening in the dreamlike state onto that with it and even Fourswords/Minsh Cap if you want (though I consider it a non-entity). Which only leaves out the ORacles, which I don't count, Phillips, which I also don't count and the NES games. And much like the ORacles games I think despite his cyncism that HateMyself was quite right some of it is just branched off of itself as the same idea with different storylines and that is the NES games and Orcale games then.
Just my theory though.
BTW the map in OOT was awesome for its day and is still great fun to explore. Though it is dated I still get a kick out of more than the much more populated and much bigger but far duller Great SEa world of Wind Waker though.