In every video game with a villain there's always a mindset goal. To me, the best of all villains are those that achieve that goal to the greatest extent. Let's put it this way:
Bowser always kidnaps the princess but he never really gets anywhere unless in Galaxy where he succeeds in almost ruling the galaxies and forming an empire.
Count Bleck comes quite close to literally erasing the entire world thanks to the Dark Prognosticus. Though Dimentio gives him the boot and takes over.
Shadow Queen rises and spreads darkness throughout the world but is defeated before the actually 'does' anything.
So overall, what Mario Villain do you think accomplished the most?