All right.

Count Dooku: The problem is the blatant hypocrisy from Dooku, so him being right about the Jedi's corruption is completely null and void when he became the leader of the CIS.

Chef Skinner: Not wrong as he wasn't aware of the rats being sapient.

Marlene: The game has shown us the Fireflies cannot be trusted and the possibility of them making the cure successfully is low.

Agatha Harkness: This segment aged poorly because she ended being worse than Wanda because she killed a lot of innocent people, including sacrificing her own child, for completely selfish reasons, primarily to gain power. (This can be blamed on bad writing because Agatha was supposed to be a "morally grey" character.

Prometheus: I don't even know where to start, his father was a bioterrorist who could have killed hundreds of people, so Queen was absolutely justified in killing his dad, Prometheus went out of his way to drag completely unrelated people into his revenge against his father, was willing to kill hundreds of thousands of innocent people, threatened to murder a child, and he ended up being much worse than his father.

Thanos: His intentions may have been noble, but the problem is that his plan doesn't make sense since he could have just used the stones to make life easier in the galaxy. And do they mean he isn't a "true villain"? He slaughtered half the population of multiple planets.

Walter and Maia Simmons: Walter never had good intentions, he only cares about humanity being the dominant race and he wanted to be seen as a hero to humanity and instigated Godzilla into killing millions in Hong Kong. Maia was fully aware of her father's actions and willingly helped him out.

Starro: Starro's brainwashing still kills its victims and still tried to kill everyone in Corto Maltese.

Darth Maul: He only cared about revenge at that point, and with that vision, he orchestrated a Mandalorian Civil War which killed thousands just to lure both Anakin and Obi-Wan to kill them both.

Chuck McGill: Chuck is the main reason Jimmy is even a villain to begin with as he bullied him when they were kids severely and went out of his way not to tell him his late mother's last words out of spite.

Killmonger: He ended up being worse than the people he hates, something T'Challa outright tells him, and he wanted to invade and conquer all major countries on the planet so Wakanda could be the greatest superpower on Earth.

Doctor Doom: I don't think CBR understands what it means to be a "Villain in the right". He still did a lot of awful things that have nothing to do with saving his mother.

Roy Batty: Nothing wrong with this one.

Ozymandias: His motives were only noble from his point of view. He automatically assumes the entire world is full of bad. He refuses to see any other option in saving the world other than his, he refuses to admit his plan is flawed and he never wanted to improve the good, he wanted to destroy the bad. He is a case of a solution looking for a problem.

Syndrome: Really? He was solely motivated by spite and egotism. He couldn't care less about the flaws in superheroes. He never actually cared about being a hero, he wanted the recognition of being one and was willing to sell his Omnidroids to anyone, including dangerous criminals.

Wicked Witch of the West: She doesn't actually care about her sister, she wanted her ruby slippers so she can rule all of Oz.

Maximus: Nothing wrong with this one.

Mr. Glass: Nothing wrong with this one.

William Johnson: He was still a Templar and the Iroquois would have to rule under them, which has been shown not to be a positive to live under Templar rule.

Kaecilius: Nothing wrong with this one.

Gorr the God Butcher: He became no better than the Gods he hates and not every god in the Marvel Multiverse is evil.

Koba: He became no better than the humans he hates and was willing to kill any apes who don't support him.

Magog: Nothing wrong with this one.

Enchantress: She attempted to wipe all of humanity off Earth and takes sadistic enjoyment in killing humans.

Illuminati: Exiling Hulk was the worst mistake they ever made as more people died because of it than before.

The Machines: They ended up being no better than the humans that enslaved them.

Pagan Min: He still ruled Kyrat with an Iron Fist and actively enabled the actions of Paul De Pleur and his sister Yuma.

Screenslaver: She still attempted to kill thousands of civilians just to frame superheroes for it, and brainwashed multiple innocent people, she is only motivated by hatred of superheroes, and not because of the flaws of superheroes.

Magneto: He was no better than the humans who persecuted him. As he wanted to wipe out all the non-mutants on Earth.

Agatha, Prometheus and Syndrome were easily the worst parts. In Agatha's case, her show didn't come out yet as of the making of the article. The latter two I don't even know what they were smoking when they wrote those parts.