I think that the X and Y either represent axes on a graph or male and female chromosomes. Coldplay's album a few years back was also named X & Y but I don't think that this will have anything to do it the game haha.

Black and White also share names with albums interestingly enough...though that's proably just by chance.

I think they wanted to go with X and Y because these are 3D games while the 3D axis is made up of X, Y, and Z, also with the added pun (sort of) of genetics which use the same letters so it's a bit of killing two stones with one stone theme here.

Also X represents mystery, while Y is another intergal, so after N we might just be getting more mathematical here. (mathematics also use Z, K, and i so there's possible third version names there but Z would fit the best imo)