The evidence would tend to suggest that there is going to be another game in Generation 6. For example, one of the theory's behind the names
X and Y' is that it is the first game in 3D, and in Maths the axis that represent 3D are the X, Y and **Z** axis. Also, Xerneas and Yveltals names obviously begin with the letters X and Y, and Zygardes starts with a Z. Zygarde can be found post-game, like Rayquaza, Giratina and Kyurem before it. Finally, Zygardes Pokedex entry mentions a hidden power' when Kalos' ecosystem is disrupted. In short, I fully expect a third title called Pokémon Z, or possibly a sequel, with Zygarde being the starring legend with new stats/forme(s), with the storyline being the disruption of Kalos' ecosystem thanks to Xerneas and Yveltal (possibly battling), and Xerneas, Yveltal and Zygarde all being obtainable.