One of the popular theories is that X and Y are based on coordinates. Which could kind make sense as the Y legendary is a bird (sort of vertical) and the X legendary is a land-based animal (sort of horizontal.) And this would probably mean the third version would be Pokemon Z.
But wait... think about this for a moment. What's special about the Z-axis? It represents depth. When you add the Z-axis, you move from 2D to 3D.
Holy crap, Game Freak if this was intentional it's truly a moment of fridge brilliance.
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I'm much more tempted to go with the theory that they're based on the X and Y coordinate planes than chromosomes, since they're making such a big deal over it being a 3D game. I have almost no doubt there will be a Z Version. And a 3rd legendary that is based off of the Z plane. I'm not sure how it'll work though. Maybe a Pokemon that can travel through alternate dimensions.
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