LoZ Ganon has an altogether hanging origin. He could be Ganon from FSA (coming before or after FSA) or Ganon from Oracles (coming before Oracles). It is unlikely that he is Ganon from ALttP. We cannot assume his origins lie in revival. Ganon is, however, referred to as the character constantly threatening Hyrule in ALttP, implying that LoZ Ganon may be ALttP Ganon, although ALttP Ganon has died. Personally the easiest way I see to reconcile this is to have LoZ before FSA, with FSA's Ganondorf reviving Ganon from LoZ, and ALttP Ganon being this same Ganondorf. This could also be reversed, with ALttP before FSA, and LoZ's Ganon having escaped the Four Sword after FSA. In any case, no game ends with Ganon in a state remotely comparable to his status in LoZ, and the question of which game Ganon escaped the Four Sword before is up in the air. He cannot be related to the Ganondorf from OoT, who has already died in both timelines.
LOZ Ganon steals the ToP from somewhere in Hyrule. This indicates the Triforce is in Hyrule, in pieces or a whole. From the AOL BS we conclude the King hides the ToC and Zelda has the ToW, which she splits. Placing LOZ before ALTTP creates uneeded explanation as to how the Triforce got back to the SR in time for the IW. It makes sense for the option of ALTTP-FSA-LOZ. Besides the part I bolded in your response doesn't make sense. Ganon's status in LOZ is simply that he is a "bad guy" who has threatened Hyrule.
There are at least two incarnations of Ganondorf, and at least three incarnations of Ganon ("incarnation" referring to "origin"--either LoZ as a standalone or to an instance in which a particular incarnation of Ganondorf becomes Ganon for the first time).
The incarnation of Ganon seen in OoT is restricted to TP and TWW.
The incarnation of Ganon seen in FSA could be related to either the incarnation of Ganon in ALttP or in LoZ
The incarnation of Ganon seen in FSA could be a revival of either the incarnation of Ganon in ALttP or in LoZ
The incarnation of Ganon in either ALttP or LoZ must stand alone (although either could be revived in FSA, as stated above)
The incarnation of Ganon seen in Oracles is a revival of any of the dead incarnations of Ganon (most likely LoZ or ALttP)
Response 1 is optional and I have stated it doesn't matter if TP/WW Ganon died or not, everything works the same way as if he survived or not.
Saying that the Ganon in ALTTP-LOZ-OOX-FSA OR ALTTP-FSA-LOZ-OOX is the same Ganon throughout doesn't create any conflict of story, it only makes things easier to explain. Ganon is born in ALTTP, returns from the World of Spirits in LOZ, resurrected in spirit by reawakening the Trident and is revived in OOX. Or he is born in ALTTP is resurrected in FSA by the Trident, escapes the FS in LOZ and is revived in OOX.
Also, ALTTP states Ganon is born during the IW and referenced as the person who has threatened Hyrule.
So the Ganon timeline, assuming OoT is first, could go like this, on either timeline, with Oracles placed after any Ganon-death (mine is bolded and underlined, yours is underlined, the typical one is bolded):
The only real plothole for either my or the typical Ganon timeline is LoZ, which is a plothole by nature. For some reason you opt for the second to last, even though it is one of the ones with the most plotholes (i.e., unrelated Ganon incarnations). Odd, considering you apparently don't advocate multiple Ganons.
You are basically listing all the possible orders of the games. The argument here is if there are mutplie Ganons and if FSA comes before or after ALTTP. Placing LOZ first provides no explanation as to where Ganon came from. Placing FSA before ALTTP conflicts with Ganon's birth and where the Trident came from, as well as why FSA Ganondorf weilding the Trident makes him the King of Darkness.