The X-Men will surely face off against some of their most iconic villains like Magneto or the Sentinels when they finally make their debut in the MCU. But there are plenty of opportunities for the movies to depart from previous screen incarnations of the franchise by using some of the X-Men's most underrated villains from Marvel Comics.
The X-Men have faced a galaxy of enemies in their near six decades in the comics, and some of the best villains are not generally known in popular culture. They also haven't been leveraged to their full potential in the comics, though that is changing for some, especially in the most recent comics, where the line between hero and villain has blurred.
Krakoa
Krakoa is the literal and figurative heart of the current era of X-Men comics, with the living island being the home for many mutants beginning in some of the best X-Men comics of the 2010s. But Krakoa first appeared as a villain in Giant-Size X-Men #1 and it remains vastly underrated as a threat to the X-Men and the world. Now reunited with its other half Arrako, Krakoa is more powerful than ever before.
Krakoa's true intentions remain a mystery, and as a sentient individual, their aims could diverge dramatically from those of the X-Men. Now more than ever, Krakoa holds enormous power and leverage over the X-Men and the world.
Proteus
Proteus is a mutant of enormous power who also has potential ties to the current run of X-Men comics, but hasn't been exploited yet. Proteus is underrated for many reasons, beginning with his vast power set. Proteus can alter reality on a massive scale, a talent that has never really been explored to its full potential in the comics.
Proteus is the son of Moira MacTaggert, the architect of the Krakoan era in the comics, and is a member of The Five, using his power to help resurrect mutants. He could do much, more more, considering his power to possess and control other people.
Cassandra Nova
Cassandra Nova is the psionic equal of Professor X, which makes sense as this underrated villain is the twin sister of the X-Men patriarch. She is so powerful that she is able to mentally disguise the fact she is inhabiting other people's bodies, as she did when she possessed her brother.
But since her debut in the Grant Morrison run of New X-Men comics, some of the best X-Men comics of the 2000s, she remains relatively low down the list of major X-villains. That could change if she were to appear in the MCU or other media featuring the X-Men.
Selene
Selene is a member of the Hellfire Club and as the Black Queen, one of the X-Men's fiercest enemies. She's also one of the most powerful. Not only is she a mutant who can draw on the psychic energy of others, but she's also one of the most powerful magicians in Marvel Comics.
Despite her enormous power and her connection with the Hellfire Club, Selene is somewhat underrated as a villain. She hasn't risen to the prominence of Emma Frost, aka the White Queen, and is mostly a background player in the comics.
Arcade
Arcade is one of the smartest and most inventive X-Men villains in the comics, and that makes him one of the most dangerous. An engineer with a tendency to build elaborate death traps and robot duplicates of himself, he almost rivals Doctor Doom in ingenuity.
Even so, Arcade remains a lower-tier X-Men villain, having never made it into the movies so far. But his off-kilter villainy and deadly methods make him unique among his peers.
Mojo
Mojo is the alien ruler of Mojoworld, a planet in the Mojoverse. The frightening and utterly soulless Mojo kidnaps people to perform in games and shows he streams for the entertainment of his minions, and has kidnapped the X-Men and their allies to make them part of his sick games.
Mojo is an extreme character in every way, perhaps making him somewhat less digestible than some of the more prominent X-Men villains. But as the MCU expands into the multiverse, he makes a lot of sense as a future threat to the X-Men and others.
Sauron
Sauron is a living vampire who drains the energy of others. He looks like a cross between a man and a dinosaur thanks to being infected by a mutant version of a pterosaur. His superhuman strength and ability to fly make him especially dangerous, and he's been a challenge for the X-Men going back to X-Men #59, his first appearance.
But perhaps due to his strong connection to the remote Savage Land, he remains somewhat underrated. If the MCU explores the Savage Land in any of its many movies or shows, he would be a great character to introduce.
Destiny
Destiny is having a moment in the current X-Men comics, returning from the dead in the Inferno miniseries. It's a great showcase for the precognitive mutant, who in many ways to now has been underrated. With the ability to see the future, Destiny is uniquely positioned as a villain against the X-Men.
Destiny has also been somewhat underrated given her importance in relation to other characters. As the wife of Mystique and adoptive mother of Rogue, she's one of the most important figures in the X-Men world.
Saturnyne
Opal Luna Saturnyne is one of the most powerful beings in the entire Marvel multiverse and is destined to appear in the MCU as it continues to explore this concept. She is the Omniversal Magistrix in charge of the Captain Britain Corps, who defend the entire multiverse. A version of Captain Britain, Captain Carter, has already appeared and is a What If..? character likely to appear in the MCU.
Saturnyne remains a somewhat tangential figure in the comic books despite her cosmic importance, often playing on the sidelines in massive events like X of Swords. Appearing the MCU would likely realize her power in a major way.
Madelyne Pryor
Madelyne Pryor is a tragic figure in the world of the X-Men. A clone of Jean Grey with all of her mutant abilities, and the one-time Goblin Queen who could alter reality on a massive scale, Madelyne Pryor is one of the most powerful villains the X-Men have ever faced.
She's largely been sidelined since her story came to its head in the original 1989 Inferno storyline but remains active in the comics thanks to clones created by Mr. Sinister. She remains a constant threat that the X-Men and readers may not fully appreciate.