Ganon's biggest flaw is that he doesn't feel like a threat. IMO BOTW2 should bring back the blood moon but make it more deadly.
Majora's Mask did this so well. The moon constantly feels like a threat especially on the 3rd day.
The timeline split has nothing to do with ganon‘s motivations, it was Zelda’s decision to send Link back in time to relive his childhood. And if your talking about the downfall timeline, that is most likely a seperate universe
But if Demise's curse were broken then future Zelda games wouldn't be able to have ganon be the main villain unless future zelda games took place before BOTW2. Ganon is as integral to the Zelda series as Bowser is to Mario.
Not that I don't want other Zelda games without Ganon though, I...