I have stated this theory a few times before. In my opinoin, two or three Ganons exist. Here is my timeline:
Base: ZSS - MC - (FS) - OoT
Adult: TWW - PH - ST - (FS) - (LoZ)
Child: MM - TP - FSA - ALttP - OoX - (LoZ) - AoL
The things in parranthesies can go in either part that game is mentioned, and that heavily depends on Ganon. Here is what I beleive. the First Ganon (G1) was born in OoT and regardless of the time, he was scealed in the sacred realm with the Triforce of Power still in his possesion. In either TWW or TP, he is released and killed. But in TWW, he might or might have not died for he was turned into stone and people turned into stone (Zelda in MC and PH) have came back before. I will get to that later. In FSA the intro states a new Exiled Ganon being born. (G2) He got the Trident and the Dark Mirror to create his minion, Dark Link. That is a larger plot point in the timeline than people realise. Link from FSA picked up the FS. When he did, he released Vaati who he eventualy killed. In the end, Ganon was scealed inside the FS. In the GBA remake of ALttP, you find out that there is a Palace of the Four Sword and that Dark Link was split into four because he used the FS. Dark Link who had never been killed in FSA must have released Ganon in ALttP which caused the Sceal War and him spliting into four. Ganon died here this time, and Dark Link once again survived, but was returned into one person when Link took the sword from him. Then, in OoX, Ganon is attempted to be revived and if you play the linked game, then he gets revived and killed. Does not make much of a difference here. Now, here is were things get tricky. If LoZ goes before AoL, then LoZ is the first appearance of Ganon 3 (G3). G3 would die in LoZ and been attempted tobe defeated in AoL. But, if G3 Does not exist, then Ganon in AoL is Ganon from FSA/AttP/OoX. And, if you remember, Dark Link from FSA/ALttP never died, so he would still be alive in AoL were he followed Link attempting to steal his blood to revive Ganon. He paniced right before he was going to get the Triforce of Courage and attempted to kill Link, but utterly died. There ends Dark Link's lifespan. If there is G3, then Dark Link2 (DL2) must have been born somewere during LoZ since Link's legacy was born in LoZ for that Link and Ganon must have acnolaged it. Now, in the Adult Timeline. He died in TWW and well, it is a little blurry there. He was absent for PH and ST. Now, if ST's sequal is FS, then LoZ does not go there. And vice verca. There is also the possibility that neither of them are ST's sequal. ST takes place in New Hyrule, which means FS/LoZ had to have taken place in Old Hyrule. In TWW, the Great Deku Tree and his Koroks were on a mission to revive the forest and execute the sea. I beleive they sucseaded. Creating new regions like the Sea of Trees which I beleive to be Forest Haven after the sucsess. As for LoZ, the Deku Tree had to have failed, but the sea had to have retreated somehow revealing the ruined kingdom of Hyrule. If Ganon in TWW did not die, and ST's sequal is LoZ, then G1 had to be the Ganon in LoZ. But if he died in TWW, then Ganon in LoZ has to be Ganon Four (G4). If he died in TWW and LoZ is not on the Adult Timeline, then G4 is really G3. Does that make sence?