First, we're not 100% sure what X and Y actually stand for in the context of the games.
Second, Z is the third axis on a 3-dimensional graph. First main-series Pokemon games on the 3DS? Yup.
The logos have DNA strands in them. That's pretty much concrete evidence the names are connected to a genetics theme.
And naming the games after the three axes makes no sense if you only reference two of them for a couple of years.
"We're celebrating the release of the first three-dimensional Pokemon game by naming the games after two of those dimensions, and then eventually the third one, making the reference unclear and pointless."
When life gives you melons, you know you're dyslexic.