The films portray Professor X as being more noble and sympathetic than his comic book counterpart, who personifies Good Is Not Nice and is a Manipulative Bastard—one of Kitty Pryde's most famous lines is "Professor Xavier is a jerk!"◊ The movie franchise takes the opposite route because Charles is a Guile Hero, one of its nicest characters (he's The Cutie in X-Men: First Class and X-Men: Apocalypse), and even when he occasionally makes the wrong choice, it's understood that he only had the best of intentions. He does get much more pompous and takes more risks with the X-Men in Dark Phoenix, but this is very short-lived. As a result, the cinematic interpretation is much more likable relative to the comics', and Xavier was purposely adapted in such a way that he became Bryan Singer's favourite X-Men character (who is a big sci-fi fan and isn't a comic book reader).
The more positive depiction of Charles is maintained in Legion, which is set in an Alternate Universe that's distinct from the movie-verse. Although Harry Lloyd's interpretation is somewhat different from the Patrick Stewart-James McAvoy version, his Xavier is also a sweetheart with a pleasant disposition and a streak of naïveté. His flaw is very similar in that he's well-meaning, yet a couple of misguided decisions lead him to become the Unwitting Instigator of Doom in the series. Thanks to his son David Haller's Time Travel, though, it's Charles—and not David, who's the star of the show—who discovers the solution to prevent David's descent into supervillainy, and after Charles persuades his son to follow the path of peace, they are able to Set Right What Once Went Wrong.
Magneto gets this treatment to a lesser extent. While he is undeniably a ruthless Anti-Villain, his motivations and interactions with others make him far more affable than the Knight Templar of the comics. Movie Magneto also has far less of a body count, and the people he does kill all pretty much had it coming especially since some of them were literal Nazis, whereas in the comics Magneto has killed innocent human life and uses the "in defense of my race" excuse whenever the X-Men or Marvel's heroes rightfully call him out on it. X-Men: Apocalypse goes the extra step further of having Mags willingly save a normal human in a steel mill; in the comics, while he can be sympathetic to human civilians, he still looks down on them and rarely goes out of his way to protect them.
Cyclops in the comics is The Stoic leader who became a Fallen Hero after several morally dubious actions and killing Professor X (albeit triggered by the Phoenix Force possessing him), and even at his best, Cyke will do anythingand make any sacrifices to safeguard mutantkind. In the films, while Cyclops is not above some occasional Wangst, clinginess and being a dick, he still has far more morality than he does in the comics. The only time he verges on his comic book counterpart is in Dark Phoenix, where he is furious and antagonistic towards Professor X, although given that Xavier had tampered with Jean's mind, he has every right to be angry.
Wolverine while a Jerk with a Heart of GoldAnti-Hero at his best in the comics, is still The Berserker whose famous quote, "I'm the best there is at what I do. But what I do best isn't very nice" (i.e. killing people), holds true. He's played the Clyde to Mystique's Bonnie for many years, committed several crimes and has killed countless people, a quite a few of whom were innocent. Although in those cases, Logan usually only killed them by accident, was unaware of what he was doing or was just simply in the wrong state of mind to notice, and he always regrets it after. In the films, Wolverine even during his mercenary or Weapon X days is shown to be a good man who does genuinely care for others besides himself, won't stand to see helpless people get hurt and doesn't always need a Morality Pet to inspire him to do the right thing, which is often the case in the comics. Movie Wolverine also antagonizes his teammates far less and is more supportive, especially to Charles.
Rogue in most other media, comics and cartoons included, is a former member of the Brotherhood of Evil Mutants who eventually pulls a Heel–Face Turn and becomes a hero. The movies do away with her villainous backstory entirely and have her meet Xavier from the very beginning.
The first four films in the franchise applied adaptational villainy to many mutant characters (most notably Deadpool and Psylocke), before retconning them into different characters to make room for more fleshed out, comic-book accurate iterations. The opposite was done for the man identified as "Trask" in the third film. Played by Bill Duke, and as the United States Secretary of Defense, he is a bit-part but has no indication of being anything like the genocidal killer robot creator of his comic book counterpart or the later Peter Dinklage incarnation, and his only role in the film is containing the genuinely dangerous mutants like Mystique, Juggernaut and Multiple Man.
Emma Frost gets this, in comics she was an amoral Rich Bitch who remains cruel and aloof even after her Heel–Face Turn to good. In her film debut Emma is a quite heroic person, as she puts herself in the line of fire to protect her fellow mutants, blocking enemy bullets with her diamond power which is a level of heroism rarely seen from her in the comics. Her villainous portrayal in X-Men: First Class is more line with her comic counterpart.
Liev Schreiber’s Sabretooth while still a villain and Jerkass is regardless far more reasonable than the Ax-Crazy beast man of the comics. In this version he genuinely cares for Logan being his older brother and instead raping and leaving of Logan’s Love Interest Silver Fox for dead like in the original telling he just fakes her death under Stryker’s orders. Sabretooth also works with Logan at the end and they part on good terms while in the comics they’re fierce enemies who can’t stand each other.
Gambit in the comics is a professional thief and loveable scoundrel, who took part (albeit unwillingly) in the Morlock Massacre. In the movie he’s just a innocent victim of Stryker and Weapon X and his hostility and suspicion of Logan is justified as believes the latter is trying to bring him back to Three Mile Island.
Harada. In addition to pulling a Heroic Sacrifice to save Logan, he's far less of a Jerkass than his comic counterpart, who is a foreigner-hating bigot.
Yukio was much more morally ambiguous in the comics (especially in earlier appearances, where she was a mercenary/assassin/thief) than in the movie.
In the comics, Quicksilver is often an outright jerk (often intentionally), but in this film, he's more of a merry mischief-maker. He can easily flee on his own once the breakout goes bust, but instead, he goes out of his way to save Logan, Charles and Erik, even though he had already freed the latter from prison by technicality. Quicksilver is also clearly not impressed (if amused) by the idea that he helped free the person suspected of killing JFK once he finds out, and is shown to be stunned and horrified by Magneto's "demonstration" in the climax.
The sequel has the Juggernaut. No, really! Yeah, he's the biggest physical threat the heroes must face, but it's all to help a kid take down the Boarding School of Horrors that tortured him and many other mutant kids. The only reason anyone wants to stop this is because in Cable's future, said kid has become a notorious Serial Killer with killing the headmaster in the present as his Start of Darkness. Zero tears are shed when said headmaster does get what's coming to him at someone else's hand.
If the character called Yukio here is intended to be the same character as in The Wolverine (despite totally different powers; she's basically Surge by another name) then she counts here for the same reason as there, as this movie's version is one of the heroes from the start.
Mystique, a villain in the comics and in the original trilogy, has been traveling the world rescuing mutants following the events of Days of Future Past, and she becomes the field leader of the X-Men. She insists that she's not a hero, though.
Comic book Quicksilver was never a member of the X-Men, but his movie counterpart is. He also expresses his veneration for Mystique's courage in defeating Magneto—his own father—and preventing the latter from assassinating President Nixon.note This confirms Peter's Reaction Shot in Days of Future Past where he was astonished—in a bad way—by Magneto's actions in Washington D.C.
Magneto ends the film as a friend of the X-Men. If he really is stepping out of the Heel–Face Revolving Door this time, it will mean he never did any of the nastier things his comics counterpart has done.
In the comic the reason why all the X-Men are dead is because Mysterio (yes, ol' fish bowl head) tricked Wolverine into butchering all his friends, sending Logan into utter despair. In film, Xavier is one who killed his students and Logan is the Sole Survivor, but this isn't a case of Adaptational Villainy for Charles since being the world's most powerful telepath and getting dementia is a terrible combination. This makes Logan's care for Charles despite what happened even more moving.
Caliban, while more of a Tragic Monster, is still quite unpleasant in the comics, having tried to kidnap and marry Kitty Pryde and even having been one of Apocalypse's horseman. In his first film appearance, he was a bit of Jerkass, but that's the worst of it. In Logan, however, Caliban is an outright Retired Monster who actively helps Logan and Charles, whom he cares for greatly, and he even pulls off a Heroic Sacrifice helping his friends escape.
In X-Men: Dark Phoenix Jean herself gets this, in the comics Jean thanks to being possessed by a Cosmic Entity becomes Drunk with Power causes a war with the Shi'ar Empire when she destroys a planet killing billions of lives and ultimately needs to be put down like a fiery cosmic Old Yeller. In the movie of the same name however, Jean doesn’t become the Dark Phoenix as the worst thing she does is kill Mystique accidentally and the real villains are the D'Bari (the inhabitants of said planet, the destruction of which was caused solely by the Phoenix Force, and before the events of the film take the place) who are expies of the Skrulls.
◊ The movie franchise takes the opposite route because Charles is a Guile Hero, one of its nicest characters (he's The Cutie in X-Men: First Class and X-Men: Apocalypse), and even when he occasionally makes the wrong choice, it's understood that he only had the best of intentions. He does get much more pompous and takes more risks with the X-Men in Dark Phoenix, but this is very short-lived. As a result, the cinematic interpretation is much more likable relative to the comics', and Xavier was purposely adapted in such a way that he became Bryan Singer's favourite X-Men character (who is a big sci-fi fan and isn't a comic book reader).
