To be fair, how many "real" and important villains does Nintendo really have. Even KKR is at least for me more of a Rareware-Villain. I know, I know. Nintendo owns him but Rareware where the ones who created him. And to be fair where also the ones that really loved to use him.
On Nintendos side we have Bowser, Bowser Jr., the Koopalings, Ganondorf, Team Rocket (the organization), Ridley, Mother Brian, Andross (and KKR if you want to count him too). Those are for me their most popular and well-known villains. Wario, Waluigi, Meta-Knight, Mewtwo, King Dedede and also Wolf I see more as anti-heroes. And others like Medusa, Ghirahim or Pokey I do not see as "All-Star villains". At least not in the same league as Bowser and Ganondorf.