I really need to dig more into ALBW's backstory for Ganon, since the ingame explanation seemed a bit off from ALttP's ending. I feel that something interesting may be there, but I just haven't gotten around to it yet.
Also, I feel that I'm one of the few who actually likes the triple pronged timeline. I always disliked that ALttP and the other 2D games were just thrown after either TP or WW, since those two games severed its original connection to OoT. Having a third branch of the timeline for OoT - ALttP seems like a more solid timeline overall.
My problem with the HH's Timeline, like most everyone's, is the explanation of the third split. If effectively makes it into a what-if scenario, rather than something that actually occurred, like the Child and Adult timelines. I suppose the upside to the explanation is that it narrows the OoX's options of placement. Since Twinrova would have been defeated on the Adult and Decline Timelines, that only leaves the Child Timeline where she is still alive, meaning that OoX would need to be placed after TP. I've made some pet theories in the past explaining how the third timeline comes to be, but there were all a little shakey, at best.
Speaking of pet theories, I still stand that the FSS could totally work on the Adult Timeline, post-ST. We once again have a continent named Hyrule, and there's no sign of the Master Sword or the Triforce. FSA already shows that Ganon is capable of reincarnating, much like Zelda and Link.