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It's centered around preventing the ecosystem from falling into disarray, which doesn't leave it much more than battling its foes. So the analogy with Rayquaza is problematic in my eyes, to say nothing of Giratina stopping the destruction of the entire universe.Rayquaza is centered around weather and atmosphere, while Zygarde's role is centered around ecosystems.
It's not as if Zygarde had anything to do with the species returning to Hoenn; it's the release of the Cave of Origin's energy that did the trick. I'd say that if Zygarde has anything to do with Hoenn, then it must have been very sloppy in letting Hoenn's ecosystem dwindle in the first place. At least that didn't happen in Kalos.I kind of took it as a possible nod and/or possible foreshadowing towards Zygarde's lore in regards to ecosystems.