This situation reminds me of Serperior, funnily enough. Serperior is heavily inspired by French royalty and aristocracy, and debuted in Gen V. Look where Gen VI's home region was - Kalos, based on France. An allusion to the future, maybe? Perhaps. Look at the beta turtle Pokemon from then Gen II artwork - widely speculated to be an early unused concept art of Tirtouga. It would not surprise me if Zygarde was designed during Gen V development but left unused until Gen VI for whatever reason.