Then what were you expecting? You're being unclear about what you, or anyone else for that matter, is expecting as far as an actual story. Do you want something equivalent to Platinum version, or even B2W2, where the third mascot essentially becomes the core of the whole story? Gamefreak somehow managed to make things work with fusing Kyurem with Zekrom or Reshiram, because it fit in with the theme of truth and ideals and it was even hinted before B2W2 came out iirc that Kyurem was basically the leftover body that remained of Reshiram and Zekrom since they were all one "being". Giratina, for all intents and purposes, was kind just there as the polar side to the dimension people normally reside in, and represented anti-matter in that regard. A story was dedicated to Rayquaza because its job was to qualm Kyogre and Groudon's complete crapfest whenever they fought.
But BettyNewbie, what is Zygarde's role and relation in how it relates to Xerneas and Yveltal? I don't want you to get the wrong impression and think I'm not disappointed that it doesn't get a story--I am--but at the same time, I've come to realize....what can it really do in the grand scheme of things? It seems that the most Gamefreak did was gave it a few new forms, maybe called it day, maybe those forms will have some use later on. But each and every time a third mascot was introduced and it had its own game, it a) either interfered with, interacted with, or caused some strife with the first two mascots of the games (Rayquaza, Kyurem) or b) In the case of Giratina (because in the games, we haven't seen Giratina fight Dialga or Palkia, he just drags you and Cyrus to the Distortion World) existed more for philosophical purposes than anything else.
So far, we can't figure out what kind of relation Xerneas, Yveltal, or even Zygarde have besides just representing different themes. Does Zygarde fight Xerneas and Yveltal? If not, does it just sit there and maintain balance between life and death? If it's supposed to have strong ties with the two mascots, then surely, at some point, there should be a Z version (unlikely with the announcement with S/M, but we'll see), but if Gamefreak somehow left it in the dust like you and others are supposedly upset about, then that must mean its purpose might be just fulfilling a philosophical purpose like Giratina did. However, what differentiates the two is that it's not hard to build a story around what Giratina represents. However, building a story on what Zygarde represents...might be a different matter altogether.