We didn't even know what Zygarde was back in XY because the signature moves, Cells, Cores and forms weren't a thing at the time, all we had to go off of were its two gen 6 Pokédex entries and Aura Break.
>When the Kalos region’s ecosystem falls into disarray, it appears and reveals its secret power.
>It’s hypothesized that it’s monitoring those who destroy the ecosystem from deep in the cave where it lives.
>The effects of “Aura” Abilities are reversed.
All you can get from those three are that Zygarde was monitoring what was happening in Geosenge Town from the deepest point of Terminus Cave and would've intervened with it's "secret power" had anything gone wrong, it didn't because Lysandre only managed to blow up Team Flare HQ with the Ultimate Weapon.
Aura Break genuinely is irrelevant to Zygarde because Xerneas and Yveltal aren't assholes that need constant wrangling like Groudon and Kyogre do, so Zygarde's ability to counter their abilities is ineffective and worthless, at most it just tells us that Zygarde believes the threat that either of them could potentially pose to Kalos is so great that it has to take precautions against both of them, which is very funny when in the same region a fucking Mewtwo was so ready to attack anything that goes near it that someone had to guard the entrance to its cave to ensure the safety of everything else nearby.
