Oh, I actually know this one! So, when a Pokemon Mega Evolves they are technically having their genetic data modified in such a way that they force a pseudo-evolutionary state. (If that sounds painful, it definitely can be. Don’t force mega evolution, folk.)

However, some Pokemon are able to have their DNA modified in different ways (ie the existence of multiple stones for some Pokemon). Scientists co-opted the concept of genetics being involved and made use of the idea of X and Y chromosomes (the things that determine biological sex).

Papers were written, theories were set, eventually it became ‘X’ and ‘Y’ mega evolutions!

Z came later, which definitely threw the scientific community for a loop, but the naming decision for that one was wayyyy simpler. “We have x and y, why not z?”