I don't see why Zygarde needs a new forme or make-over to be showcased as the cover Pokemon for Z -.- He looks perfectly badass to me~
Anyway, I'm basically sold on the idea that we'll be getting Z and not a two-game sequel like B2/W2.
I believe its involvement will be something along the lines of:
"There have been reports of random earthquakes throughout the Kalos Region. There has been no official statement, but the cause of the tremors seems to be linked to the heinous activity of Team Flare; an underground group composed of wealthy men and women united in their goal to make the world-quote, unquote-"beautiful"."
Basically, the game plays out as normal with a few differences (Tremors occurring during dialogue sequences, three or four new events related to the tremors and/or Team Flare). When you reach the climax of the story (Reviving Xerneas/Yvetal to defeat Lysandre), Zygarde emerges from the ground in an effort to stop your battling because of its effects on the ecosystem of Kalos. Lysandre simply sees the Pokemon's intrusion as another stone along his path of righteousness and attempts to defeat it, which ultimately leads to failure. It is now up to you to defeat Zygarde to quell its rage (Capturing is impossible at this point). Upon doing so, the events play out as they did in X/Y with Lysandre and the majority of Team Flare dying in the collapse of their base.
In the post-game, upon defeating the Champion and returning home, you receive a message from Sycamore via Holocaster asking you to meet him at his Lab. When you arrive, the Professor explains that he's looked into the strange phenomena surrounding Zygarde's appearance and the earthquakes throughout Kalos and has determined their hypocenter to be within Terminus Cave! He advises you to be cautious because Zygarde may still be lurking within the cave and is likely to be in an agitated state.
At this point, you can battle and capture Zygarde. However, Xerneas and Yvetal are mysteriously absent...until you show Sycamore the captured Zygarde! He informs you of two locations where the fossilized remains of Xerneas and Yvetal may be since they weren't found in the rubble of Team Flare's base.
^Gods, I ranted. ._.