I would ask you to break up the paragraphs a bit more.

I would also implore you to revisit your look at the attempts to reconcile TP in a linear timeline, since including more than two or three games in which Ganon appears in any timeline is comparatively "pitiful", looking purely at in-game evidence.

OoT-TP works well enough.
OoT-TWW works well enough as well.
FSA being the rebirth of Ganon works.

FSA-ALttP requires speculation.
ALttP-LoZ requires speculation.
The event leading to Ganon being dead in Oracles is unknown.

So, at the time, the placement of TP in-between OoT and TWW was simply a matter of looking at early intentions, and looking at the state of the Triforce in TP, and what parts of the history of Ganondorf were shown in TP, and simply shoehorning TP as some event that happened after Ganon's initial sealing in OoT.

This might have involved an all-out retcon of the OoT-TWW connection, similar to the speculated retcon of the OoT-ALttP connection, or it could have involved a complication of the transition, similar to the views of the opposite camp in the matter of ALttP. Either of these, until the nature of the events prior to TP was confirmed, was equally possible. Same is true of the interpretation involved in supposing the later-confirmed events, which we really had no evidence for, looking at TP and OoT alone.

My main rebuttal can be found in FSA itself, oddly. While you say that the nature of the Zelda universe in that game is drastically different than that in TP or TWW, what with the lack of Gerudos, and similar elements, I say the opposite. FSA is a melding of the worlds of OoT/TWW and of the world in ALttP. It is our strongest evidence for a connection between the old and the new. It carries the theme of recurring heroes and villains, what with the constant reappearances of Vaati and the rebirths of Ganon, Link, and Zelda.

I would also add that using FSA as an explanation for Ganon's return to the Sacred Realm pre-ALttP works just as well if OoT is the IW, since there would then be no need for another war before ALttP in which the Sacred Realm is sealed again; Ganon would simply escape the sword into the sacred-land-turned-prison-world, and be unable to leave.

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