i dont necessarily believe that "best" and evilest need to go together.
in my opinion, the best leader was giovanni. i like the idea of a pokemon yakuza. it was realistic. he stole pokemon away from kids, then gave them away as prizes in a casino he opened. i mean, that's just bad to the bone. also, they fucking killed a marowak.
in my opinion, cipher is the weakest. i just dont buy that whole "pokemon control time and space" shit. its too much. also, "i want to destroy the universe because i hate people and i feel like human emotions are primitive" was pants on head retarded.
i honestly feel like smaller, more relatable story like that of a pokemon mafia is more "sinister" than cell trying to destroy the universe. i mean, cipher trying to destroy the universe.