(1/15/13)
I've heard two main theories flying around about the origin/idea for Xerneas and Yveltal.
The first one is that they represent a geometrical dimension (or axis). Xerneas is said to represent the X axis because it lives on the ground and basically owns the dimension of length/width. Yveltal is said to represent the Y axis because its domain is the sky and rules the dimension of height. If there were to be a Pokemon Z, it is said that it would have the formation of a "Z" and rule underwater or underground to represent the dimension of depth.
The second theory I've heard about mainly involves the origin of Xerneas and Yveltal in Norse Mythology, in particular, the tree of life (Yggdrasil). Xerneas was apparently based on the four stags named Dainn, Dvalinn, Duneyrr and Durapror that graze among the branches of Yggdrasil at the bottom. These four stags each have a color/element corresponding to each of them, as seen in the antlers of Xerneas. Yveltal is believed to originate from the unnamed eagle who lives on top of Yggdrasil.
I have looked into both of these thoroughly, and have synthesized a third theory involving both of these, seeing as one deals with in-game storyline and the other deals with origin of the Pokemon itself. In this theory, I have kept all the details previously explained to you and added on to them. I believe that if there was a Pokemon Z, it would represent the Z axis for depth and be based on a third inhabitant of Yggdrasil, Nidhoggr. This is a serpent that lives trapped underneath Yggdrasil itself, gnawing on the roots that keep it imprisoned in the ground. Seeing as it is a serpent, it could easily form a "Z" shape with its body as Xerneas and Yveltal have done. And, believe it or not, there is a final fourth inhabitant of Yggdrasil. This creature is a small squirrel named Ratatoskr (and no, Ratata is not based off of it) who carries messages from the eagle at the top down to Niohoggr underneath. Ratatoskr might be some kind of fairy/pixie/whatever who's importance might be similar to that of Celebi or Shaymin.
(EDIT: I wrote this long before there was any word of even Sylveon, let alone fairy type. I TOTALLY CALLED THAT!!!)