If you think of X as being a flat plane and Y as a vertical plane, it makes total sense. The X legendary seems to have some kind of connection to the land (horizontal) and Y to the air (vertical). Then if there is some kind of Z Pokemon related to them it could refer to the 3rd dimension, and hey! This game's all about the 3D, am I right?
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And I'm just saying you're dumb for thinking that.
Why? If it were based off of dimensions, having a Pokemon that "created" the third dimension might happen. >_> Before then there was never a 3D, only 2D...? What? It's a video game, it doesn't have to make sense.