In my opinion the most creative villain in the Mario series is by far the
Mysterious Color Thief. Everything about him just screams creativity and tension. His identity is a mystery until the very end of the game, which kept me on the edge of my seat throughout the entire experience. His actions are vile, heartless and evil throughout. I mean, what other mario villain drops nukes on the island where the game takes place? That's just crazy.
I suppose plots where the entire world is ending due to some Deus Ex Machina Blackhole or whatever are more exciting due to their scale, but they can easily feel overdone, which to me is often the case (especially in Super Paper Mario). The actions of the
Mysterious Color Thief don't feel ridiculously overblown, they feel
realistic. They feel like actions which you could see in real life, too, making them all the more scary.
Granted, his name is a bit silly, but it works fantastically as a way to conceal his true intentions. If I were to face him I wouldn't think much of him until he actually demonstrates his power by blowing entire cities away with his nukes and draining the colour out of everyday life with his army of loyal and soulless followers.
Villains like Dimentio only stand out because their bosses, Count Bleck in this example, are absolute idiots. Their personality is so overblown that if anyone even paid the tiniest bit of attention, their plans would've been brought to an end before they even started.
Warning! Mario & Luigi: Dream Team spoilers!: show We see this in Mario and Luigi: Dream Team, when Bowser actually steps up as the party pooper and stops playing "dumb idiot boss" in front of Antasma who was trying to take control. That single move alone makes Bowser so much smarter Count Bleck and many other villains who fell for the same trap.
All in all, the
Mysterious Color Thief is a fantastic and very creative Mario villain and far superior to the overblown and shallow villains featured in so many other Mario games. Not to mention, his music kicks ass.