There are a number of debates as to just how effective mutants really work as an allegory for civil rights and racial discrimination. Critics are especially vocal in pointing out the Broken Aesop of how the mutants are colored up as "the next step in human evolution" (never mind that's not how evolution works) and find it confusing that the mutants are "feared and hated" by the general public while the other superheroes in the overall Marvel universe don't seem to have the same kind of in-universe backlash. Even the Author's Saving Throw in Jonathan Hickman's X-Men run has faced criticism for not feeling like a very satisfactory answer.
The revelation of the All New All Different Marvel line that the Terrigen Mists are now lethal to mutants for some reason, which has decimated mutants back down to an endangered species, and Cyclops has done something (that will be an ongoing mystery) to piss off the world back into "Kill All Mutants" mode, and this has made whichever mutants (that aren't the X-Men) that are still alive to pull stakes and get the hell out of Dodge. The fact that this yanks the dog's chain of the ending of Avengers vs. X-Men, turns Cyclops into an even bigger douchebag after AvX turned him into a pariah-seeking terrorist and arcs like Battle of the Atom showcased some amount of The Extremist Was Right and seriously disconnects the readers from any supposed connection with mutant hood (it's supposed to stand in for any persecuted minority, but becoming a nearly-extinct minority twice in a row with only a year or so of breathing time at the most seriously kills the Willing Suspension of Disbelief) has caused many people to decry the storyline for Too Bleak, Stopped Caring, while others are accepting of the new story set-ups despite of what is still an excess. There is also the discussion whether this whole situation, rehashing of post-M-Day as some people seem to think it is, is just more fuel to the fire Marvel seems to be pushing on to people of accepting The Inhumans as the new "misunderstood and loathed yet badass superhuman species" du jour (and with that there is massive discussions about Executive Meddling that are better off discussed elsewhere). It got to the point where very few people were rooting for the Inhumans in Inhumans vs. X-Men, which is taken as the point where Marvel started to push the X-Men once more, and established that Cyclops had been framed (for a crime that was nowhere near as great as it was made out to be, leading to more of The Extremist Was Right reactions).
Fans are quite divided about Rogue's portrayal in the movies and post-90s cartoons, where her Southern Belle and former villain characterizations are discarded to instead make her more of a Woobie and a younger student. Some fans like it as a different interpretation of character, other feel it reduced her to "an emo brat". Additionally, this had the effect of turning her into some sort of stand-in for Kitty Pryde or even Jubilee.
Whether or not Rogue should gain control of her powers is a source of argument among fans. Some feel the comics have mined all the angst they can out of her not being able to touch anyone while others feel having her gain control over her powers removes too much of her identity.
The reaction to Dazzler's visual reinvention under Bendis in Uncanny X-Men has proven divisive among the fanbase.
Iceman's 2017 solo series has gotten some of this. Some fans hated the direction and focus on Bobby’s sexuality and thought it was “too gay” and felt that his character suddenly changed and exclusively focused on his sexuality. Others felt it was true to form and fit the now confirmed closeted subtext left by his prominent writers such as Scott Lobdell and MarjorieLiu, and that the series did in fact feature many other plot points such as: the Purifiers conflict, the fake Sentinel storyline, the Champions reunion, the multiple altercations with Daken and the introduction of Amp. It was also pointed out that some exploration and navigation of one’s identity and sexuality shortly after coming out is realistic and natural. Regardless, the series sold well enough in the book market to warrant a revival in the form of a 2018 mini series and was nominated for a GLAAD award.
On the topic of Bobby’s sexuality; some were outraged and felt it came from nowhere and that it was a forced PR stunt; and others felt like it was a narrative that was true to the themes that majorly impacted the character, something which two of his most prolific writers confirmed (as noted in the entry above). The fan theories and readings that came from this intentional subtext have since been confirmed to be the reasoning as to why Bobby was chosen to be outed. Of note, Stan Lee himself approvedof it upon finding out.
Another issue bought up is the prospect of Bobby being bisexual instead of gay due to his history with women, and how him being gay would possibly contradict this interpretation. Others countered with the fact that many people come out as gay later in life, even after loving marriages with the opposite sex, and that it was rare to see a narrative that tackles such themes represented in media. Jay from Jay & Miles X-Plain The X-Men talked about this aspect here. Lastly, It should be noted that the fan theories and subtext pertaining to Bobby’s closeted sexuality have always been about him beinggay. The fact that when Jean outed him in All-New X-Men # 40 and her response to this possibility essentially reinforced the idea of No Bisexuals did not help.
Many were also outraged by All-New X-Men # 40 due to the way in which teenage Bobby was outed by teenage Jean Grey. In the issue, Jean found out that he was hiding the fact that he was gay by hearing his thoughts via telepathy, and tells him about it. However, many felt like it was an honest scene between two teenagers, with Jean in particular not having the best control over her telepathy but wanting to comfort her friend, albeit perhaps not in the most tactful of ways. Some view this as a forced outing with unfortunate implications, however others corroborated that unpredictable and uncontrollable outings with otherwise good intentions happen in real life sometimes too, and nuanced representation may still have value. This outing would later be addressed again in Uncanny X-Men: Winter’s End, where Bobby confronts Jean about finding out his secret, which satisfied many who were initially uncomfortable with it.
Scott's skull cap when in uniform, which he's had since the 60s though took a break from briefly in the 90s. For a lot of people, it's iconic and they consider it part of his look, but for others, they really dislike it, and prefer it when he has an open cowl like the 90s, or just his visor alone. What's not helped is that his hair-shape makes the skull cap look kinda like a condom (leading to a variety of unfortunate nicknames from his hatedom), while the open cowl/visor alone helps to emphasise what a Pretty Boy he is.
None of this compared to the X-mask. For some, it was a cool update of his look, but to others, it was trying way too hard and came off as ridiculous. What isn't helped is artists would have trouble deciding how to draw it, leading to it either actually covering where his eyes are to completely missing them, making it a question on how it worked with his powers.
Despite being her most popular and well known incarnation, Psylocke's Asian form is still the subject of much debate. Some fans like it and think it's cool, while some others find the idea of a white woman in the body of a Japanese person to be weirdly offensive (Why not just create a character who's culturally Asian?). There are others who find her portrayal objectifying: taking a female character who had never been overtly sexualized in her long comic history and turning her into an Asian ninja pinup babe. Then of course, there are those who like her as being a Ms. Fanservice as they consider it a character trait like any other, and see fanservice as just harmless fun and a legitimate design choice.
And then there's the whole matter of Betsy reverting back to her original body in 2018. Some appreciated it for undoing decades of weird racial politics involving the character, while other felt they should've just kept her Asian (because of how few major Asian characters there are in American superhero comics), taking away her Ms. Fanservice status when that's a defining character trait for her. Some wish they just retconned her as simply always having been that way instead.
Jonathan Hickman addressed this with the Dawn of X relaunch and is making an attempt to please everyone. Betsy will remain in her original body, but she won't be Psylocke; instead, she'll be the new Captain Britain and headline Excalibur (2019). Meanwhile, the role of Psylocke will become a Legacy Character with her former body Kwannon taking up the mantle and becoming an Ascended Extra from bit-part character to legitimate member of the X-Men and lead of the Fallen Angels comic. And yes, she wears the iconic ninja bathing suit. That said, jury's out on if this does please everyone, or just causes another case of this.
Storm and Black Panther's marriage. One part of the fandom absolutely loved the idea of wedding Marvel's two oldest and most famous African superheroes and were saddened when they broke up. An equally avid hatedom despised the idea, citing it as a case of Strangled by the Red String (as explained under its entry) and reeking of tokenism, and were ecstatic (or at least thought it was the most natural result) when the two of them later divorced after the Avengers vs X-Men event and she made it plain afterwards that it was over.
The Krakoa era. For a lot of fans, it's a return to form with lots of neat and big ideas and something of a mea culpa given the previous fifteenish years of X-Men continuity with many dead characters being restored to life and repowered and the X-Men finally getting away from storylines about being on the verge of extinction. Especially coming off of the bleak and almost nihilistic run that preceded it. But there's a good portion of the fanbase that finds significant issue with the Krakoa set up. Some points being that the status quo appeared out of nowhere, the retcon of Moira being a mutant, the rampant hedonism on Krakoa, and characters feeling massively Out of Character in general. Worst of all is that the X-Men come off at times less as heroes and more like villain protagonists, looking to protect their exclusionary ethnostate and ensure its global dominance over the human population that they seem to be, at best, ambivalent towards and are more than willing to threaten and undermine if they feel said humans are standing in their way... the kind of stuff that the X-Men fought Magneto for at his most extreme. There's even a split there among those who outright disliked Krakoa from the jump and those think things were fine originally until the story got hijacked by writers and editors who seem to unironically see Krakoa as a utopia and thus want to keep the status quo going indefinitely while allowing the excesses to be amplified.
and Marjorie