I just don't understand how one can place ALttP after an un-flood of any kind, it's like forgetting everything that happened. Hyrule just goes back to normal, the MS is found and given a pedestal and placed in the Lost Woods, Lake Hylia just goes back to being Lake Hylia, another desert emerges, and a new Kakariko Village exists again? It just doesn't make too much sense to me. The only Hyrule-based games that could possible occur after ST is LoZ and AoL, seeing as how messed up and completely different their overworlds are, which would make sense after a flood of that magnitude washes away. Heck, AoL's map has a ton of water, none of it being Lake Hylia.
I'm also sorry if this has all been said, I quickly skimmed the other posts, and didn't pay too much attention.
I personally place ALTTP on the child timeline. The people of Hyrule in ALTTP seem to know there history, pretty well.
In the adult time, the flood wiped out any historical records. Only the legend of the Hero of Time survived, and the version of the Hero of Time story that was told in Wind Waker made no mention of the Sages.
And from what we've seen of the New Hyrule so far in ST, does not seem to connect to the Hyrule in ALTTP. Plus the Master Sword is at the bottom of the ocean.
It could very well be that the Great Flood started the 'Dark Ages' of Hyrule, so to speak. After some of the waters receded, there were discoveries of new knowledge, and landmarks an such were named in tribute to the ancient land.