Baron Helmut Zemo gets my vote. He destroyed Avengers Mansion and Four Freedoms Plaza. He ruled counter earth not by conquering the planet but by saving it and earning the people's gratitude, He tricked the UN into giving him security clearance which let him rule most of the world briefly by pretending the Thunderbolts were heroes when the Avengers and Fantastic Four were in the Heroes Reborn reality. He once had the powers of every being on earth so he could defeat Grandmaster of the Elders of the Universe...which he did.
I think what sets Helmut apart from these other geniuses is he gets his hands dirty. He can take an ass beating like a flunky learn from the experience and come back even nastier. He lets it fuel him.
Some of these other guys are too lazy to do the dirty work themselves and it's usually their henchmen who get beat up while the lead bad guy flies away. Or they're too powerful. Or they do get their ass handed to them and then out come the excuses like "oh that was a doombot" "that was a clone".
Zemo's been tossed in a vat of boiling adhesive, fallen into a volcano, survived being eviscerated by Vermin, given an Aneurism by the Red Skull's daughter, had his neck broken falling off the roof of Avengers mansion, beheaded by Scourge, survived an ass whopping by Moonstone who later still fried his face off. The guy is a survivor more so than everyone else on this list with the exception of Magneto IMO. He grew up pampered then his dad got disfigured, began abusing him, his mother faked her death and left him to rot in Nazi Germany and it eventually fell to the allies, after the war he lost everything and his last name was reviled the world over.
Helmut has had to struggle way more than the rest of these guys. He put the actual work in.
Reverend Meteor (if you can tell I'm a fan)