LttP was a sequel to OoT on the AT when it was made. Placing it after TP (or anywhere else) is just speculation/theory.
Placement of ALttP is difficult. Technically, there are three possibilities:
Option 1:
----------/--ALttP--TWW/PH--ST
SS--OoT
----------\MM--TP
This won't work, because TWW backstory mentions only the Hero of Time. Thus, I don't need to post full timeline here.
Option 2:
-----/--TWW/PH--ST--(SS)--TMC--FS/FSA--(SS)--ALttP/OoX/LA--TLoZ/TAoL
OoT
-----\MM--TP
If ALttP is placed in the Adult Timeline (after TWW), then we need another Master Sword, because the old one is lost. Placing SS not before OoT, but after ST or FSA could work. There are "Gilded Guy is Vaati" theories by some people, but now (at least until more news about Skyward Sword, the game itself) my theory says "Gilded guy is (related to) Agahnim". Using FSA option, maybe Ganon (with the Trident) will appear in SS using his (different) alter-ego again? His appearance under different name than Agahnim also could work.
Also, I found that (dead) Twinrova's last quote from OoT is interesting:
I'll come back to haunt you!
Maybe she is, in fact, not really dead in the Adult Timeline, and she returns in OoX to "haunt" Link?
Excluding Twinrova (reason above) and using my Three Master Swords theory, there are only three flaws - Helmaroc King and Jalhalla in FSA (both killed in TWW, although there might be different incarnations of them, like different Gohmas), Sea Zoras in OoA (In Hyrule, they evolved into the Ritos, but maybe Labirynna is a different story?) and appearance of Deku Scrubs and Gerudos in FSA (they were absent between The Great Flood and FSA (Ganondorf doesn't count).
Option 3:
---------/--TWW/PH--ST
SS--OoT
---------\MM--TP--TMC--FS/FSA--ALttP/OoX/LA--TLoZ/TAoL
This timeline raises a couple of questions:
1. What happened with the Triforce of Power after TP?
2. In OoT - Lon Lon Ranch, in TP - Ordon Ranch, in TMC - Lon Lon Ranch again. What's going on here?
3. FSA and AoL maps - why they look like an island(s)?
4. In ALttP, the whole Triforce is present in the Sacred Realm. How?
5. If Skyward Sword goes first, what's the origin of the Hero's Clothes?
6. In some games, the same Master Sword can shoot Sword beams, in others cannot. Why?
7. Like in option 2, what's the mystery of Dekus and Gerudos? They were absent between MM and Four Sword Series (Gerudos appeared only in FSA). Again, Ganondorf doesn't count.