I listed down every MCU villain I could think of, and gave them the color/color combination I think suits them the best. You’re welcome to disagree, and I’m very curious as to why. Also, the villain from Ant-Man and the Wasp is lacking because I haven't watched that film.
Note that this contains spoilers for the entire cinematic universe.
Iron Monger - Mono-Black
CEO who only cares about gaining and retaining his power (Black).
Whiplash - Mono-Red
Revenge on Stark family for betraying his father (Red).
Justin Hammer - Mono-Black
Wants to make a quick buck (Black).
Loki - Grixis
Official statement from MaRo. Wants to rule Asgard (Black) and wants Odin to be proud of him (Red). Relies on cunning, insight, illusion, and deception (Black/Blue).
Red Skull – Orzhov
Wants to conquer the world (Black) and institute a new world order (White) because "humanity cannot be trusted with its own freedom" (also White).
Abomination - Mono-Green
Wants to be REALLY REALLY STRONG. Eh.
Killian – Rakdos
Wants to conquer the world (Black) and revenge on Iron Man and the President (Red).
Malekith - Mono-Black
Wants power. Yawn.
Arnim Zola – Azorius
Utilizes innovation and mind control (Blue) to keep the world safe and afraid (White). Not Black, as he dedicated his life to HYDRA and even sacrificed himself for its sake.
Alexander Pierce – Orzhov
Project Insight is literally just Orzhov's stated goal. "Wants peace, and also to be in control of the peace."
Ronan – Boros
Wants revenge on Xandar (White/Red).
Ultron – Azorius
Constant self-improvement and innovation (Blue) plus a need to exterminate Avengers on moralistic grounds/exterminate most of humanity and guide the survivors (White).
Yellowjacket – Rakdos
Wants to sell Pym particles to terrorists (Black) and driven by vindictiveness towards mentor (Red).
Zemo – Mardu
Main Red. Wants revenge for what happened to his family (White/Red) and is completely unfettered (Black).
Kaecilius – Orzhov
Different kind of Orzhov villain. Worships Dormammu (White) and wants immortality for himself (Black) and everyone else (White).
Ayesha - Mono-White
Ruler of society with extremely rigid caste system. Wants to kill the Guardians to prove that no-one messes with her.
Ego – Jund
Wants growth (Green) and companionship (Red), but is too narcissistic to care about anyone besides himself (Black).
Vulture - Mono-Black
A unique take on a mono-Black villain, for once. Wants a comfortable life for himself and his immediate family.
Hela - Mono-Black
Wants to conquer the universe, and is unafraid to kill even her own people to do so. Also a necromancer.
Grandmaster – Rakdos
Hedonist. Wants to dominate Sakaar (Black), and acts according to his whims (Red).
Killmonger – Mardu
Wants revenge on white people (White/Red) and to rule a new empire with himself on top (White/Black). At his base, just a kid throwing a temper tantrum.
Supreme Intelligence – Orzhov
Wants to conquer the galaxy (Black), but wastes resources on a genocide just because it doesn't like people resisting it on principle (White).
Yon-Rogg - Mono-White
Just a space Nazi. Yawn.
Thanos – Orzhov
Official statement from MaRo. White is because of balance and moral code. Black is ambition for better universe + willingness to achieve it at any cost.
Note that this contains spoilers for the entire cinematic universe.
CEO who only cares about gaining and retaining his power (Black).
Whiplash - Mono-Red
Revenge on Stark family for betraying his father (Red).
Justin Hammer - Mono-Black
Wants to make a quick buck (Black).
Loki - Grixis
Official statement from MaRo. Wants to rule Asgard (Black) and wants Odin to be proud of him (Red). Relies on cunning, insight, illusion, and deception (Black/Blue).
Red Skull – Orzhov
Wants to conquer the world (Black) and institute a new world order (White) because "humanity cannot be trusted with its own freedom" (also White).
Abomination - Mono-Green
Wants to be REALLY REALLY STRONG. Eh.
Killian – Rakdos
Wants to conquer the world (Black) and revenge on Iron Man and the President (Red).
Malekith - Mono-Black
Wants power. Yawn.
Arnim Zola – Azorius
Utilizes innovation and mind control (Blue) to keep the world safe and afraid (White). Not Black, as he dedicated his life to HYDRA and even sacrificed himself for its sake.
Alexander Pierce – Orzhov
Project Insight is literally just Orzhov's stated goal. "Wants peace, and also to be in control of the peace."
Ronan – Boros
Wants revenge on Xandar (White/Red).
Ultron – Azorius
Constant self-improvement and innovation (Blue) plus a need to exterminate Avengers on moralistic grounds/exterminate most of humanity and guide the survivors (White).
Yellowjacket – Rakdos
Wants to sell Pym particles to terrorists (Black) and driven by vindictiveness towards mentor (Red).
Zemo – Mardu
Main Red. Wants revenge for what happened to his family (White/Red) and is completely unfettered (Black).
Kaecilius – Orzhov
Different kind of Orzhov villain. Worships Dormammu (White) and wants immortality for himself (Black) and everyone else (White).
Ayesha - Mono-White
Ruler of society with extremely rigid caste system. Wants to kill the Guardians to prove that no-one messes with her.
Ego – Jund
Wants growth (Green) and companionship (Red), but is too narcissistic to care about anyone besides himself (Black).
Vulture - Mono-Black
A unique take on a mono-Black villain, for once. Wants a comfortable life for himself and his immediate family.
Hela - Mono-Black
Wants to conquer the universe, and is unafraid to kill even her own people to do so. Also a necromancer.
Grandmaster – Rakdos
Hedonist. Wants to dominate Sakaar (Black), and acts according to his whims (Red).
Killmonger – Mardu
Wants revenge on white people (White/Red) and to rule a new empire with himself on top (White/Black). At his base, just a kid throwing a temper tantrum.
Supreme Intelligence – Orzhov
Wants to conquer the galaxy (Black), but wastes resources on a genocide just because it doesn't like people resisting it on principle (White).
Yon-Rogg - Mono-White
Just a space Nazi. Yawn.
Thanos – Orzhov
Official statement from MaRo. White is because of balance and moral code. Black is ambition for better universe + willingness to achieve it at any cost.