We dreamed of creating the world's strongest Pokemon... and we succeeded.
~ Dr. Fuji's last words (about Mewtwo).

Some villains aren't born; some of them were created by a mad scientist, insane psycho, or others who just want someone else to do their dirty work for them. Some of these creations may not have been made for evil, but something happened to the creation and turns evil, like the Indominus rex and Ultron.