>>53624999X are the unnatural looking evolutions, taking the line in a different direction, while Y take the lines in a direction that accentuates the existing traits.
Mega Charizard X becomes Dragon, getting blue flames, while Mega Y continues the direction the line was headed by developing its Flying attributes.
Mega Mewtwo X adds a Fighting type, taking Mewtwo from a Special Attacker to a Physical one, while the Mega Y, looking more like Mew, further develops the Psychic traits.
I don’t really see a connection with Xerneas and Yveltal other than the color (X=blue, Y=red).