Also, I felt that X & Y may be more about genetics than geometry... The basis in which the Pokémons will be made stronger will be changed, also we got a glimpse of that kind of concepts in B&W2 where Kyurem merged with a Pokémon(Zekrom or Reshiram). Also, by the looks of the legendaries, X looks like a god of life, while Y, with it's many hands look like an everlooking god of death.
It may be as simple as 3D coordinates... But it would be fairly stupid if it was the sole significance.
Well if I happen to be wrong then I'll buy the X version on the cheap when the next Pokémon games are announced (thereby ensuring there will be no third version).
I also wanted to clarify that my original response in this thread was answering the question "Which version looks cooler". I really can't say which I'll buy until I know all the differences.
@Davoid Oh, I imagine it has a double meaning. The games can't really focus on just one axis (1D games? Whoa!), so they're doubling it as chromosomes to fit into the story as well as the symbolic meaning of being 3D. The third version may not actually be called Z Version, who knows, maybe it'll be XX or XY, but there will definitely be one, just as there always has been one.
Our group tends to negotiate with each other, forming pairs when the release of a game like this nears. So... both I guess, multiple times over. Although personally I'll take X because CARIBOU!