I'm really hoping there's an extensive quest that makes us look all across the region, in every nook and cranny, to find the four cores and all the cells to create our Zygarde--that kind of emphasis on exploration is what I wanted from a hypothetical "Pokémon Z," taking full advantage of how cool and unique Zygarde's form-changing method is. It would be even better, in my opinion, if it was at the center of a plot-driven post-game narrative. It would be neat if some Kalosian NPCs made some important cameos during that time, too. But if there's a way to intertwine Zygarde into the main plot, I wouldn't be opposed to that, either, although I do feel at this point it's probably best left for the post-game.
I feel we'll need to gather the cells and cores together, perhaps using a Key Item to store them, and bring them all to that Yggdrasil-like tree to have them come together and try to capture our Zygarde. If the cores each take up a space on our party, that could add to the challenge, which could turn out interesting if they mean for this to be a complex endeavor. I wouldn't mind if it was a challenging quest, because Zygarde Complete seems absurdly powerful! It would be very fitting for the quest to obtain him to be difficult.