I suppose it's quite a crackpot theory but I do really like the idea of them adding another 72 or so new Pokemon (this batch could have a new legendary trio that is so far missing in Kalos) in the third version for this generation. Sort of like a 6.5 gen. It's something that would definitely catch fans by surprise and would be out of the ordinary. I feel like the idea does have some weight to it though, after all Zygarde is likely to be the mascot for these games and its X pokedex entry states:
"When the Kalos region's ecosystem falls into disarray, it appears and reveals its secret power."
As most of us probably know, ecosystem refers to a community of living organisms. (fauna/flora etc) It's possible this might be the plotline for these games, the Kalos ecosystem falls into disarray. Zygarde gets upset and possibly lashes out at those who destroyed the ecosystem. Then unleashes it's secret power. If an ecosystem falls into disarray in real life, attempts might be made to introduce new species to balance it. (although I can't say I know much about this subject)
I actually had another theory that Zygarde would create numerous green blob guys and they would transform their DNA permanently into Pokemon species that perished during the war. So Zygarde would have a sort of natural DNA bank within its body. (
https://en.wikipedia.org/wiki/DNA_bank)