I just initially assumed it's to do with graphs and that we're to expect a third version called "Z". As in the X and Y axis, and the Z axis which allows us to represent shapes on a graph; third dimension.
My other thought initially was that it would be representative of chromosomes, but the colouring is wrong; surely the X would be red, XX is female, whilst the Y should be blue, XY is male. That could just be me being picky, though.. but even so, if it is to do with chromosomes, how would they implement that into Pokémon? I don't think it really.. has a place, unless I'm being a bit too closed-minded..?