So as we know Mewtwo was designed sometime around 1995-1996 when Pokemon Green was being developed. As we know Dragonball Z finished its original broadcast run in Japan in 1995. Pokemon like all videogame or anime series were likely heavily influenced by Dragonball Z.
At the time both Mewtwo and Freeza debuted, they were considered "the most powerful beings" in their universe. Mewtwo started off as a villain or final boss in the games, Freeza is the main villain of Dragonball, and both were heavily promoted in similar white and purple color schemes.
And of course later on both Mewtwo and Freeza are then surpassed by other powerful legendary pokemon or characters in their series, whereas now Mewtwo and Freeza need new transformations (Mewtwo has two Mega forms, Freeza has Golden Freeza) to keep up.
I think it's pretty obvious myself, most of the GameFreak designers likely grew up with Dragonball when they were kids or teens.