It could, I guess. Not should, but could. The sprite / design is kind of stretching far. It is kind of hard to come up with a purely X shaped design, at least to the extent as Yveltal's Y design.
Further, it goes a little beyond just the shape of the Pokemon. Xerneas is the more 'feminine' of the two, what with being Fairy type and all. This might imply something regarding chromosomes (Female being XX whereas Male is XY), whereas Yveltal, the more 'masculine' is associated with the Dark type. Stereotypical? Probably. However, it does make sense.
It's further important to note that this is a game made for the younger kids, so it's probably like, to quote a book, looking for depth in a shallow stream.
Besides, without its stately neck (which imparts the Y shape more than anything), you gotta agee, Xerneas looks kinda dumb.
Sorry, my MS Paint skils are rusty at best.
Xerneas, along with Yveltal, was designed by art designers Ken Sugimori and Yusuke Ohmura. Initial design for the two Legendary Pokémon was started by Sugimori, but he encountered "artist's block", having a hard time coming up with concepts. For the first time, he gave the work over to another designer, Ohmura. Ohmura furthered the designs, after which Sugimori resumed to finish them.
So you can tell they were running out of ideas.