The idea of X and Y being a meaningless title is disturbing, and I doubt they'd do that just to throw the entire world off. Anyway, a Z sequel could tie into both the 3D theory AND the genetics theory, because the Z chromosome does exist in the ZW sex determination system. It's a bit of a stretch, but still plausible (and I hope to god that there is a genetics component to the plot, because if there was I would figuratively DIE OF HAPPINESS RIGHT THEN AND THERE); the ZW system determines the sex of birds, some fish, reptiles, insects, crustaceans, etc.
But I digress. I've got to say, if it happens it would combine two of my great nerdy loves, genetics and pokemon, and I don't know if I'd be able to handle all of the feels. And you know it's serious, because I never say "all of the feels."
EDIT: Call it too much bio if you want, but the X&Y germ theory is also something to chew on. If you look at the neuron and myosin shape, you really start to see Xerneas and Yveltal.
There's a bigger version of the picture, but I didn't want to stretch the board.