These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
The Magus is probably among the most powerful foes any X-team has ever faced, and the New Mutants squad, the Professor, and a cosmically-powered Carol Danvers ended up stopping him. And Doug Ramsey was the guy who won the battle.
Ensemble Darkhorse: Rahne has been a member of more X-Men spinoff teams than any other character.
Hollywood Homely: Skids was considered "ugly" by the morlocks. This, of course, is because the Morlocks are all hideous and consider her a freak among freaks.
Ho Yay: Arguably Warlock towards Cypher before the latter's killing-off.
Still present after Cypher came back. "I love you and you are breaking my heart." Well...
Between Shatterstar and Rictor as well
Les Yay: Danielle and Rahne, due to their psychic-link when Rahne's in wolf-form.
-and a good deal of obvious subtext, calling each other 'soul-mate', a revealing event in the Inferno-alternate Manhattan, and Dani saying as much as 'I love y-' on a cliff in Scotland.
Sometimes, Illyana towards Kitty, too.
Moral Event Horizon: Pierce crosses this several times in the New Mutants origin story alone. Examples are ordering the death of Dani's grandfather and having his men trying to kill each of the New Mutants who were, at the time, teenagers who had only just discovered their powers.
The Ani-Mator also crossed this by killing Cypher.
My Real Daddy: Warlock and Legion were introduced when Bill Sienkiewicz was on the book, and due to his unusual art style they have never looked right when they were drawn by other people (most artists just copied his style for that particular character, which caused them to jar with their surroundings). This isn't so unusual with Warlock due to his nature as a being of twisted organic metal; but Legion looks really strange (see The Muir Island saga in Uncanny X-Men for an example).
Bird Boy is probably the most extreme, being an imbecilic half-animal who derailed the book into whacky antics and over-eating. He's actually one of the most-accurate in-continuity versions of the Jackovasaurs from South Park. At least he was rapidly Put on a Bus.
An entire team of Scrappies was folded in following the Inferno event with the X-Terminators: Boom Boom, Rusty, Skids, Arty, Leech, Rictor, Whiz Kid. Luckily the bulk of the characters were quickly put on various buses, leaving Rictor and Boom Boom to become beloved members of the group, though this derailed the book from a thoughtful angsty series into the very "mall-going brats" adventures that old-school fans thanked the old writers for not using.
They Changed It, Now It Sucks: The level of "dumbing down" from the earliest issues to the time of Cable's leadership is so marked that it also marks the beginning of the Liefeld Age of comics; chrome arms, pouches, guns, pointless angst, no-character writing, teeth-gritted action, "ninjas appear from the future", etc.
They Wasted a Perfectly Good Plot: Cypher was a polarizing character amongst fans of the title in the 1980s, in part because he had sensible everyday mutant powers in the form of the ability to understand any form of language, which sadly also made him utterly useless in fight scenes unless he merged with the alien Warlock. So when Chris Claremont left the book and Louise Simonson took over, Simonson decided to kill off Cypher since she didn't feel like coming up with excuses for why he was MIA in fight scenes, plus felt that no one liked him. Sadly, when she killed him off, fans revolted against the death. Even the fans who were calling for Doug to be killed off! And to this day still fans rant and rave about how Cypher had so much potential that was utterly wasted by Simonson misreading the room.
It's a real shame that Doug was killed before the internet became near-universal or he could have been the world's greatest hacker.
Cable versus Apocalypse/The Twelve, which was the replacement for the Highlord Ascension storyline when it was dropped, was haphazardly aborted for a lame-ass month-long event called "Ages of Apocalypse" involving the X-Men in different time periods play-acting various scenarios.
Tear Jerker: The issue that dealt with Ilyana's death - or, rather, Jubilee's reaction to it. Even the knowledge of Comic Book Death and the likelihood of Ilyana's eventual return wasn't enough to dampen the emotional weight of a tale about a little girl slowly dying as the adults around her slowly come to the realization that there's nothing they can do to help. Although "I won't allow her to be placed into a living death!" isn't a good argument when it might have allowed them time to find a healer and it certainly would have allowed time for her brother to get home before she died.
The Woobie: Rahne. A couple of her old teammates have had worse backstories, but few radiate please hug me as much as she when they are down over it.
If there's one constant with Karma it's that life seems to find a way of crapping all over her and her specifically.
Crowning Moment of Funny: In the new series, Dani gets her friend - a congnitive therapist - to try to work around the personal issues of her teammates and Nate Grey. She has to explain to him the Summers Family Tree.
X-23's Odd Friendship with Dust, which leads to the former going to considerable lengths to save the latter from Stryker and his Purifiers.
Nate Grey is getting those in the new series, first with Cyclops assuring him he is finally home and second with Hope Summers taking him under her wings, despite all the issues she must have with his pressence.
Cult Classic: The DeFilippis/Weir run. The later Kyle/Yost run has a more traditional sort of fanbase.
Ensemble Darkhorse: The Hellions, to the point that not only they got their own mini, but under Kyle & Yost series basically became "Surge and Hellions", before the cast expanded.
Pixie and Rockslide under Kyle & Yost - since cancellation of New X-men they are two members of the cast most used. Megan even got her own limited series and Santo had huge supporting role in Wolverne & Jubilee miniseries.
Fan-Preferred Couple: Elixir/Wither, for both the obvious and the fact that their powers cancel each other. But mostly the obvious. Wither is also more commonly paired with Mercury than his canon crush, Wallflower.
Flanderization: Combined closely with Demoted to Extra - a common complaint by fans of the characters is that since New X-Men ended, Julian and Noriko only show up whenever writers needs somebody to act like a jerk to main characters, Victor has been reduced to token gay character and Santo exists solely to say something funny from time to time.
Sympathetic Sue: A candidate for the most messed-up backstory of any X-character.
The Scrappy: Icarus. You'd think this would be because of acting like a moron and inadvertently getting himself and half his friends killed in the first Kyle/Yost arc... except nobody much liked him under DeFilippis and Weir, either. Perhaps he still had the stench of the infamous Chuck Austen Uncanny run (the first run to prominently feature him, though he'd been a background Guthrie child in older comics) about him?
Strawman Has a Point: Kevin Ford (AKA Wither) is hiding out in a junkyard after accidentally killing his dad with his disintegration abilities. While trying to lay low, he ends up killing the dog belonging to the junkyard's owner. A confrontation ensues, and at the last second, Dani Moonstar rescues Kevin and beats up his attackers. While we're supposed to root for Dani and not the bigoted junkyard owner, it's hard not to sympathize with him given that a mutant just trespassed on his property and killed his innocent pet. And then when Wither decides he doesn't want to stay at the school, after having no on-panel counselling or training to control his powers, and after having to be stopped from deliberately killing someone, Xavier just lets him go on his way. You're supposed to be on Xavier's side for letting a kid choose his own life, but when the kid has already killed someone and his mutant power is dissolving any organic matter he touches, you kind of feel like getting the cops involved might be a good idea, and maybe the pro-registration crowd have a point.
The Woobie: Oh boy, does it have several. At the end of Kyle and Yost run you can say all of students are this, having been put through so much their definition of good day is "nobody has been killed or maimed today".
Iron Woobie: Pixie, hands down. What she went through with Kyle and Yost was only the start of hell other writers subjecter her to, yet she never loses her smile.
Jerkass Woobie: Hellion is a bit of a jerk, even if with heart of gold, but not only DeFilippis and Weir had his parents effectively disinherit him, under Kyle and Yost his life has been turned into endless series of kicks in the face. And then they kicked him even more in X-Force. Surge and Prodigy could also qualify, considering some questionable choices they make in last arcs, that are directly caused by what they've been through before.
YMMVs for Young X-Men:
The Scrappy: Ink was hated by many fans. The fact that the writer went to extreme lengths (like, you know, giving him the power of Phoenix) to make him seem important did not go over well with fans, and he also had the stigma of being a human rather than a mutant. Being a Jerk Ass and bizarrely ending up with Emma Frost in a Bad Future also didn't help.