Guys you're thinking too much bio. D: I don't know but I'm way too exposed to physics and math, so my other theory was the one Isasapiens suggested:

X and Y are coordinate axis to represent the series's jump to 3d.

I'm thinking that the whole reason they made it X and Y is related to the x-axis, y-axis and z-axis being the conventional names for the three axes in a three-dimensional Cartesian coordinate system. So if there's a third version, I think that's gonna be Z if this theory holds. I mean it's for the 3DS. A three-dimensional system / three-dimensional dual screens thingo. So I think it sort of makes sense. :\

Plus chromosome theory suggests that the third version not be Z, imo. If anyone knows more biology than me then they should correct me, but I don't remember any other chromosome at the same league as the X chromosome and the Y chromosome. :(

A 3-D graph has three axis' X,Y, and Z. X and Y are only a 2-D graph.

Well if they make a Z then it will still work as a reference to the three-dimensional coordinate system, I suppose. :p