1. Charles Xavier, The Hulk-Busting Hypocrite
Professor X might just secretly be the greatest villain in the X-Men milieu. That may sound ridiculous given Chuck is meant to embody tolerance, hope, and coexistence in Marvel's favorite mutant family. Consider for a moment, though, that at nearly every turn he's tried to sabotage each and every one of those very ideals.
His first, and arguably most egregious, act of self-treachery occurred during the Deadly Genesis storyline. Well, technically it started in 1975's Giant Size X-Men #1: the story which introduced the world to longstanding X-people Wolverine, Storm, Colossus, and more. The reason being because someone needed to save the original team of X-Men from a walking, stalking island named Krakoa.
Except these weren't actually the "someones" the prof had in mind. Deadly Genesis retconned this classic tale such that Xavier actually sent in another second team ahead of the ones you know and love. A team which died a horrible, violent death. With the exception of a liberated Cyclops -- who realized he had a secret, equally super brother just in time for his sibling to get slaughtered -- the team was pretty much pounded into dust. Not wanting a black mark on his PR campaign Chuck covered up this hilarious hiccup with psychic shenanigans and sent more meat to the grinder.
Years later Professor X lost his composure again. This time badly enough to try and kill Magneto by drinking his brain like a mutant milkshake. The act of psychological murder unfortunately (and predictably) backfired and turned the combined pair into the super-killer Onslaught. Which as you can imagine was not a great look for the symbol of human-mutant relations.
While this was happening Xavier was also playing hypocrite with the lives of beings he decided were too dangerous to play with the rest of society. When the world's baldest psychic himself bit the dust himself his will and testament revealed that he had been secretly brainwashing a man since childhood to keep his powers under control.
He did the same thing -- though with less telepathy, and more drugs and experiments -- to his infinitely powerful and mentally perturbed son David. Not to mention the Hulk, whom he helped fire into space because that was obviously a surefire plan. Oh, and he helped kidnap the first natural-born mutant in years and sent her hurtling through time. The list goes on, and rarely will you find a bullet point that paints Chuck as anything but a self-centered schemer.
2. Tony Stark, Fascist to Futurist and Back Again
Tony Stark's questionable deeds are a bit more obvious than most. He was a weapons designer, after all. One that started out rich and got to be even more-so by building better killing machines for the U.S. military. Given the country's usual policies on high-powered weaponry (i.e. using it bunches and bunches) you can probably lay more than a few thousand bomb and bullet victims and the eventual Iron Man's shiny metal feet.
Whatever! A change of heart was had, and Tony Stark put an end to all that imperialist nonsense. Weeell, that is until the Illuminati rolled around. Writer Brian Michael Bendis's clever send-up of the white, male kings of privilege painted Stark as exactly that: someone who thought he and he like-minded, like-everything friends should be in charge of the world's affairs. That whole, disastrous episode with the Hulk getting shot into space? The Illuminati.
Then came the much talked about superhuman Civil War. With a name like "Civil War" readers had a pretty good idea of what the crossover would be about long before it started. What they likely didn't expect was the mostly moderate Tony Stark going 110 percent bad guy during the event. After fighting against superhuman registration -- the key conflict in the story -- Tony waxes nostalgic for his fascist fraternity days with The Illuminati. He pulls a 180 on the issues and becomes the first poster child for unmasking.
After which Mr. Stark helps Reed Richards, patriarch of the Fantastic Four, build a robot Thor clone to Astroturf support for the movement. So far, not-so-great on the old campaign trail. It gets worse when the robo-clone puts a hole through an Avenger's chest.
Then worse still when Tony and company start shipping off dissidents to the Negative Zone. That particular land of sunshine and honey being home to homicidal alien bugs and not much else.
Tony's tendencies up to this point weren't entirely the character's own fault. Marvel star Mark Millar is as unskilled a scribe as you could hope to find when it comes to politics, which made his run during the entire Civil War event less than coherent. Though Iron Man writer Matt Fraction apparently recognized this, and wrote Tony into a corner that caused him to reboot his own brain. This "new" and downgraded Tony Stark found was unburdened by the twisting morality of multi-character events. That is until the next time a crossover turned him evil.