I really, really can't see the genetics idea coming true, for a few reasons.
One - X isn't female, and Y isn't male. XX is female, and XY is male (at least in humans, for birds, for example, it is reversed). X is called Turner symdrone, and Y is... well, dead (you need the information on the X chromosome to live).
Two - Look at the legendaries. Even if they were going for a gendered motif - does Xerneas look feminine? Does Yveltal look masculine? No, not really. However, Xerneas does look like an Earth spirit and Yveltal looks like a sky spirit, which suggests that the inspiration is the dimensional axes, X and Y.
Three - To be honest, genetics, especially realistic genetics, doesn't seem like something that'd ever get brought up, if for no other reason than they'd pretty much have to explain how Pokemon breeding actually works.