He horrifically mutated an innocent Pokemon into a monster
He captures and sells living creatures as prizes in a casino
He created his own Pokemon species for the sole purpose of making a profit
He intentions are purely greedy.
He wants to rule the world through fear and raw power
He's slain countless innocent Pokemon at the Pokemon tower just to get an item that will help his plans along
Even after he's gone, his grunts still cling to him and respect him, if not fear him
The fact that he is the final gym leader blew my mind as a kid. Pokemon just doesn't have serious villains like Giovoni after GS. I mean, Team Aqua/Magma were just silly, and DP just copied the story of RS.
Even the anime makes him a cold heartless bastard in the first season.
You can laugh and go "lol pokemon" but the story of Mewtwo is really demented and sad. Mewtwo is even a
really disturbing looking Pokemon, even after they redesigned him to not be so freaky looking.