There are mainly three big speculations considering the namesake of X and Y. Everyone's noted the obvious mathematical schematic. X axis and Y axis, Xerneas being the
running or
lateral and Yveltal being the
rising or
vertical. The biological aspect, as you mentioned, could extend further backward from blastulaic germ layers; namely the sex chromosomes.
As for the other fan-theory, which I find much more plausible, is more of a mythical basis. Since we can safely assume Gen VI region to be based on France (and Europe by extension), Xerneas and Yveltal bear similarity to creatures of Norse and Celtic mythos. In the image linked below, you can see the three levels of Yggdrasil. Up top is the
Wyvern, notably, Yveltal. Xerneas is represented as a culmination of the
four stags of the middle realm (Note the four colours on Xerneas' antlers). Which lends itself to the third creature, a serpent, which very much could be the basis of a possible Pokemon Z title.
http://www.kimikogaming.net/wp-conte...y1tco1_500.jpg