Xerneas is a deer.
The deer is an important figure in Celtic mythogoly, and modern neopaganism.
Celtic relgion also revered nature, which Xerneas is known to be associatied with.
The Gauls, the pre-Roman inhabitants of France, were on of these Celts.

Yveltal bears a resemblance to an eagle.
The eagle is a symbol of the Roman military; the Aquila.
Yveltal's main colour, red, is also a symbol of Rome.
Additionaly, Yveltal is associated with the sky, and the most powerful Roman god; Jupiter, was lord of the sky.
The Romans conquered early France, and mixed their Latin culture with the native Celtic culture to create French culture and language.

On the right side of the Kalos map, one can see what appears to be an aqueduct.
Aqueducts were constructed by the ancient Romans, and many still dot the French countryside.

On the top left of the Kalos map, one can see what resembles the Carnac stones, as well as Stonehenge.
Both of these are believed to have been built by the ancient Celts.

So, if X, Xerneas, a land creature who represents the Celts; and Y, Yveltal, a sky creature who represents the Romans;
Who could Z be?

Nearby to the Celts and Rome were the German and Norse tribes; who eventually conquered Rome.
In ancient Germanic mythology, there is a serpent called Jömungandr.
Jörmungandr was a massive, evil, aquatic snake who encircled the world, much like the great rivers and seas of Kalos encirlce it.
Should Jörmungandr ever stop encircling, Ragnarok, doomsday, would occur.

Similarly to how Xerneas and Yveltal are shaped like their letters, one could easily design a snake-like creature to be shaped like a Z.

So, we have;
X-Xerneas, a land and nature spirit, representive of the Celts;
Y-Yveltal, a sky spirit, representive of Rome;
and Z-Jörmungandr, a water, and possibly evil spirt, representive of the Germanic tribes and Doomsday.

Much like the Germanic invasions spelt doom for Rome, Jörmungandr may spell doom for Kalos.