I subscribe to the theory that we'll find out about them when Zygarde becomes the feature mascot of a third game.
Right. Pokemon Z HAS to happen sometime after the remakes are made! Every time a remake Pokemon game has happened, there was a 3rd version to go with the two games released before the remakes, but in the same gen. Example: Emerald. Was only released AFTER the remakes of 1st gen was made! Platinum: Was made in the same Gen HeartGold & SoulSilver (you know what those are a remake of), and Diamond and Pearl was released. We only got sequals for 5th gen instead of a 3rd version, because 1. It was released on the same system Generation 4 was on, and 2. was released without a remake to happen. Judging by GameFREAK's patterns of how and when they release their Pokemon games, I've come to the conclusion we will get a Pokemon Z after ORAS is released. It may take awhile, but I can see it truely happening. Also, we know about Yveltal and Xerneas, but we know almost NOTHING for a true fact about Zygarde!
I have this theory I made-up though: Zygarde's job was to protect the ecosystem, when Yveltal tried to destroy everything, sucking the life out of every living thing! Zygarde did it's best to try to stop Yveltal from doing that, but with the power of "The Ultimate Weapon" having been fired, it could do nothing to stop it, due to the power being too strong for it to handle. And so, it hid in the cave you find it in, keeping watch of the ecosystem from it being below in that cave. Should the ecosystem be threatened ever again, it will rise-up, and stop it from ever happening again. Because you stopped Team Flare from using Yveltal for utter destruction from them using the Ultimate Weapon (Which would kill every Pokemon on the planet if it had worked), Zygarde had no reason to rise-up, and use it's Aura Break Ability to destroy the weapon from within! Zygarde would been able to stop it in time this time, as it had seen it been fired-off once before. So it would have seen it coming!
I imagine that if Pokemon Z DOES come, the weapon would have been closer to firing-off, and you would need Zygarde this time to stop it (ala, Pokemon Emerald's Groudon VS Kyogre's battle needing to be stopped by getting Rayquaza's help, using it's ability to cancel weather effects. At least, that's what I think happens, I've never played the game, ya see?) by using Zygarde's Aura Break. Also, they may pull-off a Black & White 2's style of getting the 3rd Legendary, and make you wait till you defeat the Elite Four and Champion, before you can get Zygarde. Well, that's all. Hope I didn't make any spelling errors and/or any other errors. Sorry this is a long post guys...