From: Dark_Zoroark | #003 Thatīs not the problem, is just that FSA has Ganon and the games prior in the Split 1 do not.
And I donīt buy that SS-MC-FS-OOT, MC-OOT map is completely nonsense. First a desert in SS, then a swamp in MC and FS and then a desert again in OOT, come on!
That is the problem, because Ganon is the reincarnation of Demise's curse, and thus has to be in a timeline where that curse took place. You said that timeline 1 is where there is no curse. Ganon appears in FSA. --- "As I was walking up the stairs, I met a man who wasn't there, he wasn't there again today, i wish I wish he'd go away."
To clarify... You've got the Four Swords line off in its own separate branch based on an understandable misinterpretation of what happens with SS's time travel (I understand how it can seem that way and it threw most of us off at first, but it is just simply not what they intended), and then... And then you've still got the controversial three-way split of the official timeline anyway? (Plus the edit of separating the Oracles as a different Link again. (I don't really like that either, but it is officially LttP Link in them.))
If you're going to fudge with the official timeline in some way, I prefer what I came up with.
My idea would involve a split in SS as well, but it's not what you might think. I think that there is a flaw in the self-sustaining time loop such that, instead of it just simply being one universe that creates the conditions for its own creation, there is a split over a seemingly minor detail and the two near-identical universes create the conditions for each others' creation. In my theory, that difference is the existence of the Tree of Life. (Although I couldn't really come up with an adequate idea for why the Link in the universe that has the tree would need to go back and NOT plant the tree. So I was just thinking that he collects a fruit from it and then the tree seems to begin to fade from existence so he goes back to investigate, sees nothing wrong, returns but finds himself in the world without the tree, and then shrugs it off because he already has the fruit anyway.) Both universes lead to the same conclusion and eventually to the same events in ages after that... up to a point. I was thinking that somehow or another the presence of the tree tips the balance in OoT. Maybe Ganon picks a fruit from the tree and eats it and it makes him just a little bit stronger than he was on the universe without the tree, and that is where the "Link fails" ending of OoT comes from. (That ending is not really a split out of OoT. It is the ending to a near identical parallel universe's version of OoT, the universe where the Tree of Life exists at the end of SS.)
Anyway, could they have done something different with the game to somehow explain their intentions better? Sure. (Although it's not like the clues weren't there. We can see the crystal in the temple before Zelda goes back, and Granny was wearing Zelda's bracelet the entire time as well.) Make the wording a little different here or there. Perhaps edit the scene before they return to their time to clarify that Impa puts the sword back into the hidden space below the floor to keep it hidden (and also to add in the part that we're assuming must happen where the sealing spike is created).
Regardless, the intended meaning of the events in SS is that nothing was ever actually changed in the past. They only went back and played their parts in what had already happened. Demise was only partially destroyed, and the leftover part was resealed with the creation of the sealing spike after we left at the end.
(Hell, the very notion that his mind is trapped within the Master Sword at the end? That right there already contradicts the notion that he was destroyed completely anyway. But it can also be suggested that because the revival was still ongoing (it was not complete so long as Zelda was still alive) only a part of his essence was released and formed into the body that we destroy.)
I might try to go into some of my thoughts on the overall map of the series as well, but I'm going to need to use another post for that. (It'll go way over what's left of my limits for this post.)
edit: See my posts here for my thoughts on how most of the maps in the series fit together.