I did consider RSE and my assumption (beyond "Zygarde didn't exist yet") was "The problem was Kyogre and Groudon. That's Rayquaza's fix, Zygarde ain't one to step on another legendary's toes (unless that other legendary is the problem)." Heck, maybe Zygarde is the one who tasked Rayquaza with being Kyogre and Groudon's mediator, since as you said they are very extreme ecological disasters.Zygarde is a lore problem for RSE and B2W2 too because Kyogre and Groudon are about as extreme as ecological disasters as you can get and Team Plasma's Kyurem powered cannon being used in a plot to freeze the entire Unova region kind of threatens that region's ecosystem.
I think the real answer for why Zygarde didn't show up is because shut up. :P
Putting it more seriously, the lore between games is kind of loose so Zygarde not taking action is probably going to be a plothole in later games too.
I have a similar thought regarding DPPt, though it's less "that's Giratina's problem" and more "what can Zygarde do against Arceus's direct underlings?" (even though I think Zygarde is stronger competitively, in-game strength does not always match lore.)
I hadn't considered B2W2 at all. I considered B1W1 and went "Ghetsis's plan would suck for humans but wouldn't really affect the ecosystem" and then completely forgot that the script changed in the sequel.
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