It cannot take place between
OoT and WW for these reasons.
1.) The end of
ALTTP blatantly shows us that the Master Sword will never again be used, so it cannot take place before any game with the Master Sword, including WW.
2.)
ALTTP ends with the total destruction of Ganon, so he could not have been alive in order to escape the Sages' seal prior to WW.
3.)
OoT =/= the Imprisoning War, because
OoT does not involve Ganon getting stuck in the Sacred Realm after wishing on and obtaining the full Triforce.
4.) No hero appeared between
OoT and WW.
It cannot take place any time AFTER WW for this reason.
1.) At the end of WW, the Master Sword is buried beneath the Great Sea, along with all Hylian culture. Because Hylian culture is all over the place in
ALTTP and the Master Sword rests within the Lost Woods, this game cannot take place after WW.
It CAN take place any time after
TP for these reasons.
1.) The Master Sword is seen resting in the Lost Woods in
TP, setting itself up perfectly for
ALTTP.
2.) The Seal War is not an issue, seeing as no game has ever accurately depicted it, regardless of what the developer intent was
11 years ago.
3.) A new Ganon can still emerge after
TP, seeing as his "essence" has been known to survive after Ganondorf is killed, and this would make sense if
FSA happens after
TP, but
FSA still isn't necessary in this equation. Every aspect of the Imprisoning War can take place completely offscreen in between games.
4.) The Sages' seal spoken of in
ALTTP may not have anything to do with Ganon at all. It only referred to sealing the Sacred Realm because evil was flowing from it. Which could have taken place at any time, even before
OoT. So by
TP, the Seal War could still have occurred, seeing as
ALTTP's canon backstory says Ganon got stuck in the Sacred Realm quite a while AFTER the Seal War.
5.)
ALTTP was made as a distant sequel to
LoZ and
AoL, in which the Triforce was NOT in the Sacred Realm. So the text where it says "still rested" means nothing.
6.)
TP connects loosely with OoX, with the Noble Sword being in the Lost Woods before being powered up to become the Master Sword, Midna was quite clearly designed with Veran in mind, and Twinrova isn't dead in OoX, and she died on the adult timeline. She never died AT ALL, as far as we know, on the child timeline, explaining why she is alive in OoX. Which
may prequel
ALTTP with
FS/
FSA in between.
7.) The Interloper War could very well be the Seal War. We know it involved dark corrupting powers being used to try to conquer the Sacred Realm after people began to "Quarrel and fight" and a "great battle ensued," where the back stories of
TP and
ALTTP are pretty much identical up until this point. The efforts of the Interlopers could very well have been responsible for the evil flowing from the Sacred Realm, so as the Knights of Hyrule and the Sages took care of the evil, the Light Spirits and Goddesses handled the Interlopers personally.
8.) The above war would then end with the creation of the Temple of Time and the Master Sword, explaining why they exist in
OoT and this works, because the Sages created them as a seal on the Sacred Realm. And you could argue that the Sages' seal of
ALTTP was designed to keep evil in and not out, whereas the ToT does the opposite, but why can't it do both? Just because the Seal failed with
OoT's Ganondorf doesn't mean it failed with
ALTTP's Ganondorf.