Alright time to fight bad good guys.
The Leader:(Your-Movie-World)

Doctor Doom
Yeah, blah blah, everyone else here also chose Doom, but only because he’s the best fit. He isn’t the strongest, but his leadership is undeniably good, and he is very clever.
The Dragon:
Thanos is very cunning, intelligent, and powerful. He has knowledge of both magic and technology, with shields powerful enough to withstand one hit from Galactus, and he also beat the crap out of a very angry Thor going all out.
The only reason why he isn’t the leader is that he’s his own weakness and will probably think up plans that fail. Having Doom as the boss means Thanos won’t do that.
The Speedster:

The Runner
The Runner is durable, has super reflexes, and super speed that exceeds the Silver Surfer. The Runner will just outright speedblitz most characters, but he’s an arrogant guy, so not perfect.
The Powerhouse:

This guy is really strong. While escaping his own people, the Osirans, he nearly slaughtered the Milky Way Galaxy, and also single-handedly destroyed most of the Osiran race, forcing Horus to lead 740 Osirans to finally take him down.(Your-Movie-World)
While paralyzed and with his powers heavily weakened and suppressed, Sutekh’s mental ability easily punched through the TARDIS shields, a feat only replicated by the Big Bang! Other than that, he’s shown some extremely powerful feats, such as destroying a planet by pointing at it.
And he does it while casually mentally restraining and dragging the Destroyer, another Doctor Who villain that eats planets.
Sutekh: (Amused) You've convinced the colonists to fire on us?
Bernice: As many as I could. Enough I imagine, to obliterate this pyramid and everything in it.
Sutekh: Are you sure I can't withstand it? Just as I've withstood everything else.
Bernice: I'm betting you're new body hasn't stablized just yet. You're still tender. Vulnerable.
Sutekh: Vulnerable? I was never that. I am tempted to prove it, but...why take the risk. I brush them aside, they mean nothing to me. And as for the colonists...
(Missiles and bombs falling)
Sutekh: They are all gone. Their toys fall from the sky, their war done. Let their guns grow cold. Let their homes gather dust. Let their bodies rot. I am Sutekh bringer of...peace.
He also kills everyone on Mars with a thought. Even the Time Lords, a race that manipulates entire universes like toys, cannot stop him should he ever break free from the prison.
The Evil Genius:(Your-Movie-World)

The Master
Yes, they’re all the exact same person, yes even the woman.
The Master is a renegade Time Lord who’s decided that he/she wants to rule the universe and be Master of all (though his arch-nemesis the Doctor doesn’t exactly think the Master is really close to as threatening as Omega, Rassilon, Sutekh, Monica Lamprey etc.). The Master is extremely dangerous, possessing the Time Lord package of super reflexes, hypnotism, increased strength, speed, and durability, and his greatest ability: intelligence.

The Bogeyman:(Your-Movie-World)
Well, you gotta have a bogeyman capable of getting rid of all the pesky people trying to get you. So my ‘bogeyman’ will be…
The Then and the Now

Perhaps the most OP bogeyman in fiction, the Then and the Now is the bogeyman to Time Lord children. It’s a walking impossibility of a paradox, a very hole in reality, in existence, in the layers of the Time Vortex that surround the Multiverse. Time itself abhors the very existence of the Then and the Now. It can travel through time, stop a TARDIS and its presence causes extreme pain to time-sensitive and precogs, and it proceeds to fracture the timestream by being there. And not.
The Oddball:

The Memeovore
The creature was unlike everything. It required an effort of will to even look at it. It was a void, a chasm, an absence made visible, it was everything made nothing. Faced with it, the brain rushed to fill it with detail, any detail, a black world-devouring octopus, a spider with eyes the size of Mars, a crooked cube unfolding, a ruined city cluttered with insane memorabilia, a cartoon character with eye sockets crammed with worms. Phantom images projected by the tottering brain into the yawning absence of the creature.
Can’t post a picture because nothing can understand a Memeovore. The Memeovore is a Devourer of Concept, of Meaning. Created by the Time Lords, it was meant to hunt down the Fendahl, known as the Ultimate Predator. It succeeded in its task.
The Memeovore was also used as a weapon by the Time Lords in the War, but it immediately went after the universe of pure concept, Mictlan, where the Celestis, a race of pure thought and concept, lived.
The Memeovore doesn’t destroy planets, or cities, or stars. It destroys meaning to those places. It ate the concept of speech for a New Quintesson, and they never noticed any difference. It ate the concept of kinship for another planet, and the concept of colour on another, the concept of texture in another, and the concept of culture, and the concept of thought itself.
Finally, the local region of conceptual space shattered and drained, the predator withdrew temporally bloated. In its wake, a billion souls lay on ground whose textures they could no longer understand, unable to think, unable to feel, unable to hear their own screaming madness as anything more meaningful than white noise.
It then devoured Mictlan, which as you remember is pure concept, destroying the Celestis. The Time Lords then chopped the entire chunk of space-time out of the universe into the Void, where the Swimmers would eat the Memeovore and what was left of Mictlan.