The evil of spoilers,however (Ending spoilers)Ganon dying was expected, and he really never dies anyway
My timeline theory is this Aonuma loves timeline while Miyamoto doesn't, Aonuma's games, MM and WW, are heavily connected to their predecessors in the timeline, and theres no question about their place, while Miyamoto's games are loosely tied, its just more proof how Miyamoto was so deeply involved in this game that it really doesn't fit in the timeline that easy.
But it really looks like this game is part of the MM timeline, after all OoT Link returned to a world without ganon being imprisoned, without a splitted triforce and all that, so my guess is in this timeline after MM ganon got hold of the triforce anyway, splitted the triforce, was twilight imprisoned and then TP occurs, and luckily the wii zelda game, with less Miyamoto influence will connect all 3D Zeldas by joining the two timelines.
What Im almost sure is that MM is connected to this twilight realm, after all, its said that the mask was banned into shadow because of its powers, that corrupted certain tribe that Im almost sure is Midna's. Yes Im basing this solely on the fact that the fuse shadow has an eye thats just like the one in the mask.