Slightly disappointing, but not unexpected. Better luck next month.
Eh, it's more aestetics than readability, at least in my opinion. Having two different games on the same console use practically the same pokemon for the cover seems extremely bland. And again, it part of creating the legendary pokemon involves creating stuff for the story, it isn't much of a net loss of time since you are getting two things that need to be worked on done at the same time. I'm pretty sure that they'll run out of ideas for regular pokemon before they run out of ideas for legendaries, and stories involving them, due to the amount of mythology/stories they can pull from. Heck, if they do make the titles relevant to the story, there's a plethora of Sun and Moon Gods and godesses they can pull ideas from, since those were fairly common objects of worship.
As for making good use of Zygarde... What kind of main story arc could you envision with it playing front and center? It's power seems to be related to revitalizing the Kalos ecosystem in case it goes out of wack, which doesn't seem to be something that an evil organization would covet too much. Perhaps if the way it fixes the ecosystem results in mass destruction and genocide... but that would be two different antagonists with the same kind of end goal back to back, which would be kind of dull. (Considering Lysandre is as dead as Norwegian Blue in a Monty Python skit, it would have to be someone different.) Perhaps a Delta Episode-type side story arc could be done with it, though. However, and maybe I'm wrong but, I don't see there being enough there to make a story that doesn't step on the toes of XY's story.