>>28382555While that's true for the most part, I think there has been small instances of what I described in my 1st post to some extent.
For example, I know that a part of Lysandre's dialogue in the XY climax changes slightly depending on the game, as the legendary of X represents life and the legendary of Y represents death. I think in one game he ultimately tries to kill MC&friends, while in the other he tries to turn them immortal but leave them trapped in their base forever.
Imagine if in SM you have collected all zygarde cells before the climax and that alters slightly what a specific character says or how an event goes. Something small and simple like that would be enough integration in the story for me, but I'm ok with it either way, having Zygarde itself is already cool enough.