I always thought that Ganondorf was the same character in every game, I'm not sure if this is actually stated anywhere, but I figured he's always resurrected/not fully defeated because of the triforce of power he has, and also
because Skyward Sword implied that he's incarnated with Demise's hatred, which would always come back or whatever.
And if that's the official timeline that Zero Kirby posted, I find the three alternate timelines thing kind of ridiculous. If there's just going to be a ruined timeline where Link gets defeated no matter what, there'd be no point for him to even travel to the future, he could just immediately travel into the past as soon as he got the ocarina of time and warn the king that Ganondorf was about to fuck everything up. The adult timeline doesn't seem to have a reason to exist, haha. Then again that might be more of a problem with OoT's story than with anything else, and I have to realize I'm critiquing the mythology of a video game series, one that might not have originally meant to have a concrete timeline anyway.
Three timelines raises some more questions, though... with the split timeline, does only the timeline of Hyrule diverge, or is the split all-encompassing? Are there three separate iterations of the sacred realm and goddesses as well, even though they're apparently all powerful beings? If not, do they oversee all three timelines? How does that work? Would Hylia be aware of it, or
any incarnation of Zelda after the split, considering she's Hylia's reincarnation? Is Demise's hatred affected by the split?
Does the twilight realm from TP exist outside of Hyrule's timelines? Is Termina destroyed in the two timelines without Majora's Mask? Considering all the time-altering magic and artifacts in the series, is there any way the timelines could interact or affect each other?
Once again, I'm probably reading too far into this, haha.