Hmm, that's an interesting point. If I remember correctly, there are canonically 5 Zygarde Cores (at least as far as Alola's concerned), which would initially seem at odds with Aevium's four Subregions… until you remember that Terrial is further split into two drastically different landmasses. I figure that there'd be one Core per landmass, so my guesses are...
Floria: Route 4's fancy new Wild Area (a place that big and unspoiled by man's bound to attract an ecosystem-defense system, after all)
Terrajuma: Part of the jungle we don't currently have access to (somewhere down the river beneath the Lover's Bridge, perhaps? ); Valor Mountain's also an option, but that place is packed to the brim with events already...
East Terrial: Somewhere in Route 9, either beyond the two NPCs that have been in that absurdly long conversation (seriously, it's been almost a week in game, minimum...), or in the cave system.
West Terrial: the quicksand-filled cave (this is the one we already have, BTW)
Neverwinter: ...We've never been to any part of this place (assuming Blacksteeple isn't in its waters, of course), so I naturally can't guess for this one
Generally speaking, it seems unlikely that Zygarde would want to put it's most important parts near Garufan territory given their tendency to... mistreat the laws of nature in dramatic ways, but it also wouldn't want to be too far away as to keep it from springing to action should they pull anything dramatic enough. Of course, I'm not a partially-connected deific hivemind spread across several hundred miles of land, so my thought process might be a bit off here.