In an alternate Marvel Universe, there are no heroes or villains. The lines are blurred. The heroes and villains as we know them have formed their own cabals that rule delineated parts of Earth. Which group will ultimately prevail in world domination?
The Brain Cabal (Location: Americas): Reed Richards (and the rest of the Fantastic Four), Bruce Banner, Tony Stark, Victor Von Doom, Nick Fury and T'Challa
The Power Caba (Location: Space, Moon, and Ocean): Sentry, Thor, Namor, Ms. Marvel and Blackbolt (and the rest of the Inhumans)
The Mutant Cabal (Location: Europe and Asia): Magneto, Apocalypse, Vulcan, Wolverine, Emma Frost (and the Stepford Cuckoos), Iceman, Storm, Mystique, Forge, Cannonball, Colossus, Multiple Man, Elixir, and Darwin
Since Millar's run is not in continuity and MoD was never referenced in comics outside of it, there are no MoD upgrades for Doom.
:-P
Also, mutants stomp. They have Forge and Magneto and Poccy on their side, they can assemble whatever doomsday device they need much faster then anybody else.
Probably the Brains tbh. They probably already have plans for most of their opponents. Like when Stark cloned Thor. He had the DNA to be used for years. That's how cunning they are.