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.
Is Wolverine-As-Leader a reluctant leader burdened with The Chains of Commanding? Or has he been turned into a Drill Sergeant NastyCanon SueHypocrite that routinely bullies subordinates (who are, of course dissenters and thus always wrong) and has abandoned integrity to his principles in a stunning display of the fact that power corrupts? Both interpretations have supporters and detractors and a respectable amount of evidence can be assembled for either interpretation. Coupled with the fact that pretty much every fan of X-Men has their own personal preferred characterization and canonical references (and the fact that Wolverine's characterizations have often been wildly varied even within the same source) and things get rather messy, rather quickly.
Similarly, is Cyclops really a Fallen Hero and Heartbroken Badass struggling to put his life back together, or is he just a chump who rode other people's coat tails? Or even worse, is he a violent, Too Dumb to Live, psychopathic YandereMan Child, crippled by an unhealthy relationship from his teen years that he should have outgrown? Or does he just need a hug? There's really not a lot of evidence to back him up as the X-Men's former leader or any kind of competent hero or even a decent boyfriend for either Jean Grey or Emma Frost.
And while we're at it, is Jean Grey really Cyclops's one true love, who gets understandably upset at his serious temper problem and barking orders at her instead of saying sorry? Or is she just a shallow, manipulative, insecure bitch who took advantage of Cyclops's loneliness and poor self-esteem in order to feel better about her own shortcomings (whatever those may be)?
For that matter, is Xavier really a loving surrogate father figure, to Cyclops and the X-Men in general, or is he just a manipulative, ruthless bastard who kicks people to the curb - namely Cyclops - when it suits him? Or was Xavier giving Cyclops the cold shoulder an attempt at "tough love"?
Was Emma Frost really such a horrible person for going along with the Inner Circle/Hellfire Club's plans and just exploiting Cyclops, or was she in fact the One True Love of his life who tried to save him from an unhappy work environment?
Even the MRD - Mutant Response Division - is up for this. Are they really a bunch of pure evil Fantastic Racists who believe the only good mutant is a dead mutant, or are they misguided but genuinely Well-Intentioned Extremists forced to take up the sword to protect the innocent from violent, psychopathic mutant terrorists (the human flip-sides of Magneto in other words)? Are they just mercenaries and hired guns who don't care who the target is as long as they get paid to do what they do best, or are they vengeful Death Seekers, men who have been genuinely wronged by mutants (having lost friends and loved ones to mutant attacks for example) and now seek to kill as many mutants as they can before they go out in a blaze of glory? Or are they a mix of all these possible groups?
Anti-Sue: Cyclops is this to Wolverine's Black Hole Sue and other various assorted Marty Stu tendencies. Wolverine's flaws are glossed over to the point that they don't exist while Cyclops's flaws are dialed up so high that he can't even function properly.
Asspull: While not a big offender in terms of plot, the show has an asspull in the fights between Wolverine and Sabertooth. Since a fight between two guys with healing factor and razor sharp weapons would be far too messy for a children's cartoon, their fights end up being relatively anti-climatic. The asspull comes in their first encounter when Sabertooth pulls a giant taser gun nearly half as big as he is out of his cloak, despite there being no bulk or any sign of it when you can peek into his cloak before. Making it look like he actually pulled it out of his rear end.
Cyclops also has some of this going for him. Some fans absolutely loved how this version was the complete opposite of the Standardized Leader that Cyclops usually is, some even go so far as to say that this Cyclops being so genuinely flawed made him more interesting than Wolverine for once, if only because he actually had flaws to struggle with. Other fans however absolutely hate this version of Cyclops for being the complete opposite everything the character has ever represented and for being degraded to nothing more than a pathetic loser who's been a useless twit all his life and having no real character development towards becoming a better person.
Complete Monster: The Shadow King, from "Overflow," is a cruel and merciless telepathic mutant who forced a child Storm to be a thief and would berate and threaten her if she did not bring back enough stolen goods. Xavier befriended Storm and defeated the Shadow King. Though his body was destroyed fighting Xavier, his evil spirit lived on and he gained the ability to possess others and force them to do things against their will. When we first see Shadow King in the present, he has possessed a starving man in a desert. When another man comes to help this starving man, The Shadow King possesses the good Samaritan and leaves his original victim to die in the desert. Shadow King later possess Storm herself and forces her to use her Weather Manipulation powers to destroy all Africa, simply to spite her.
Cyclops appears to be this. The show insists at least once or twice that he used to be some kind of hero, but he is never portrayed with any sympathetic traits and never really achieves anything.
The X-Men as a whole may count given that they don't get to be heroic very often.
Designated Villain: Weirdly enough, Cyclops seems to qualify for this as well (or alternately Designated Evil). The flashbacks of Breakdown reveal that when Wolverine first arrived at the Xavier Institute he hit on Jean Grey almost immediately with no regard for whether or not she was in already in a relationship, and then proceeds to mock and taunt Cyclops, which then leads to Cyclops blasting him repeatedly until Jean got in the way and chastised him, saying Wolverine wouldn't fight back because he promised her he wouldn't fight Cyclops. Now sucker blasting Wolverine when the clawed one wouldn't fight back - and apparently when he'd only been there for like a night - doesn't portray Cyclops in the best light, but Wolverine was the one who went after Jean, acting like a horny biker guy more interested in a hot one night stand than in anything resembling true love, AND it was Wolverine who was clearly goading Cyclops into a fight. The look in his eyes, the tone of his voice, Wolverine was clearly daring Cyclops to take a swing at him, probably figuring he was all bark and no bite (which turned out to be hilariously wrong) so... how exactly is Cyclops the bad guy here?
Maybe because blasting someone in the back hard enough to knock them down for taunting something that would never happen is downright scary? Hell, it's what many Muggles in X-Men in general fear. A super-powered mutant losing his cool and hurting others. Jean also didn't know that he was goading him, or that he didn't know about the promise.
Evil Is Sexy: Selene and, if one considers them evil, Domino and Rogue. Also Sybil Zane.
Fan-Preferred Couple: Scott and Emma ironically enough. Or not, considering they'd been together in the comics for almost ten years up to that point and the fact that Jean Grey, Scott's Designated Love Interest, was not portrayed in a sympathetic light.
Growing the Beard: Concept art shown and scripts leaked for Season 2 implies that this would be the case. But of course it never saw the light of day.
Idiot Plot: The entire basis of the series revolves around the idea that Xavier would seriously trust Wolverine of all people with the safety of the X-Men and the future of the entire world.
This gets worse. Xavier makes Wolverine leader in the same episode that shows Wolverine is a poor leader. He takes the whole team to Genosha to fight Magneto when he learns Xavier is there. Beast points out there is no evidence that Magneto attacked them a year ago, and they should try to talk Magneto first, since Magneto is the ruler of a nation of mutants who are utterly loyal to him. Logan ignores his suggestion completely. He takes the Blackbird out when Forge is still repairing it. Instead of waiting for Forge to finish his repairs, he risks the entire team's lives by having them fly it, while Beast and Forge work on to keep them in the air. It's clear he has no plan or strategy in mind. His actions get the team captured and at Magneto's mercy; if it weren't for Magneto not wanting to kill them, they would be dead. Magneto points out how foolish Wolverine's actions were. Wolverine accuses Magneto of trying to keep Xavier locked away, while Beast plays mediator and asks if they can take the professor, which Magneto allows. At the end of the episode you wonder why Beast isn't made leader, since his advice showed he doesn't let his emotions cloud his judgment and was more reliable than Logan (who in this series was noted to go off at random and come back to the mansion whenever he pleased). While it's debatable if Logan grows into a better leader as the series goes on, this episode still makes you question why he was chosen to be leader over other candidates in the first place.
And on top of that, it's revealed in a later episode that Wolverine hadn't even been with the team that long when the mansion was destroyed - literally one night or at least implying as such (creating a Continuity Snarl) - which just makes Xavier putting him in charge even more ridiculous.
An entire episode revolved around the X-Men being too dumb to fend off a bunch of rinky-dink ninjas.
The Shadow King crossed this line before the series even began, forcing Storm to be a child thief and threatening to kill her for not bringing back enough stolen goods. He only gets worse from there.
Warren Worthington II crossed it by ordering the MRD to go after his own son, then ordered the doctors to amputate Angel's wings, just so he can make his son normal. Worthington refused to understand what mental and emotional pain it would cause his son, and it went back to bite him when Sinister transformed and brainwashed Angel into Archangel, who became bent on revenge against his own father for taking away his wings.
The above moment also counts for Colonel Moss, who took blatant pleasure from attacking Angel and showing no remorse upon finding out that it was Warren II's son.
Mr Sinister is revealed to have crossed it when we learn his plotting leads to a future where Apocalypse rules over a dark Social Darwinist nightmare future where his survival of the fittest creed is unchecked. Before this, in series anyway, he was merely a thoroughly creepy schemer. It's hard to find even the smallest bit of sympathy for a man who knowingly ushered in hell on earth.
The Inner Circle - Emma believed they were still going with the original plan of destroying the Phoenix Force by depriving it of a body and releasing it into the atmosphere; the new plan involved a transplantation from one body to five in an attempt to control it as a weapon of global conquest. And notably, the second they reveal this to Emma, she turns on them immediately.
Jean yelling "Scott! What are you doing?! It'll kill you!" when Cyclops tries to fight the Phoenix in the final episode comes off being more unintentionally funny than dramatic and intense due to the way the normally reliable Jennifer Hale's voice squeaks and cracks as she delivers her lines. Not helped by Jean's lack of an actual characterization and the poor quality of how her relationship with Cyclops was depicted.
Pretty much any scene where Cyclops yells, due mostly to the normally reliable (though miscast) Nolan North going very over the top with it - though given the overall characterization of Cyclops he probably had no other option.
Cyclops's whole characterization and in particular his origin episode Breakdown is so full of Narm it almost isn't funny.
Shadow King is by far one of the darkest villains in the show, even trying to raze Africa from sheer pettiness.
"Hunting Grounds" gives us the Hunter that Mojo has been preparing. It turns out to be a Brainwashed and CrazyWolverine, incapable of rational thought and with a creepy-as-hell Slasher Smile fixed on his face à la The Joker.
Mister Sinister transforming Angel into Archangel. The moment when his victim's face realises what exactly he has done is both terrifying and heartbreaking.
Older Than They Think: A mutant with Armor's near-exact ability actually showed up as part of the Asteroid M story-arc in the 90s comics, even making an appearance as one of Fabian Cortez's cronies in the X-Men: The Animated Series two-parter that adapted said story.
Ron the Death Eater: Boy, does Jean get no end of this. It seems there's not a single action she's done in the show she hasn't been condemned for when many actions are actually quite understandable. Her so-called hypocrisy of being pissed at Cyclops shooting a guy in the back in retaliation for a taunt of her being interested in him, a lie, as compared to her getting pissed and tying someone down for full-on making out with her unconscious boyfriend.(Which, admittedly was one of those "I might never get the chance" type of things, but she sure didn't know that and most don't take the time to ask questions when they see someone macking with their unconscious lover.) Her action towards Wolverine, which the former is often compared to? Blowing Wolvie a kiss. After Cyke blasted the guy in the back, rudely confronted her and insisted on having a talk instead of apologising for losing it. Yeah, not quite the same. Several even make theories that Jean was brainwashing him to love her despite there being not a shred of evidence, just a single instance of telepathic flirtation which is presented as such.
Rooting for the Empire: With Wolverine in full on Canon Sue mode, Cyclops an unsympathetic Jerkass, Xavier an unlikable Manipulative Bastard, and most of the X-Men reduced to non-entities, it's kinda hard NOT to root for Magneto and the other various villains, if only because they have more personality and pizzazz.
Ship Sinking: Somehow happens to both Jean Grey and Emma Frost in regards to Cyclops.
They Just Didn't Care: For a show that was supposed to be all different and edgy and unlike any X-Men cartoon ever seen before...the series recycled a lot of familiar beats, and the writing was surprisingly, painfully sloppy more often than not. Including, but not limited to, squandering precious episodes on Wolverine having G-rated fights with The Incredible Hulk, the entire X-Men team (sans Nightcrawler) being kidnapped by ninjas, or a Narmtastic butchering of Cyclops's origin. And, when they weren't busy failing to offer any kind of logical reason for why Wolverine just had to be in charge, they were wasting time rehashing the Dark Phoenix Saga, the Hellfire Club/Inner Circle, the Shadow King and Days of Future Past - and not even doing a good job rehashing them. And this isn't even getting into playing up movie stereotypes like Wolverine being the center of the X-universe and being the one true love of Jean Grey, Rogue's go to guy for familial support and one true surrogate son and heir to Professor Charles Xavier, despite the fact that he apparently spent even less time with them in this show's universe than he did in the movies.
The animation and character designs, while not terrible, are nothing special either. Where past X-Men cartoons managed to give everyone their own unique and distinct look W&TXM's designs are all pretty much identical, to the point that after a while you really do feel like you're seeing the exact same face that was simply stacked onto a different body and given different eyes and different hair.
They Wasted a Perfectly Good Plot: Cyclops's fall from grace and eventual redemption could have been an important and compelling arc, and adapting his controversial romance with Emma Frost could have made for some great tension between him and the other characters. But his intended character development never really kicks in and by the end of the series he is somehow back together with Jean Grey, without even showing a proper reconciliation between the two. No apology from either, no tear-jerking confessions, just there they are, back together.
This becomes more painful when the X-Men anime had a similar character arc for Cyclops where he falls apart after Jean's death, but deals with it and leads the team. It eventually builds up to Cyclops realizing he has to live in the present and move on, while cherishing his past with Jean, and leading the X-Men in the climatic battle. While both versions of Cyclops started him off as closed off and jerk ass-sh, the anime version still socializes with his teammates (plays pool with Wolverine) and can put Jean issues aside to still lead the team properly. Here, Cyclops' character arc never reaches that conclusion, despite them trying to build up to it.
Wolverine being pushed out of his comfort zone as the loner and being forced to be a responsible leader never really amounts to anything interesting either.
Storm is not only one of the most powerful X-Men, but also one of the group's leaders. In various continuities she has lead the team when Xavier or Cyclops can't. While her not becoming leader makes sense to the plot (she wasn't present when Xavier made Wolverine leader) you would think her leadership skills would make her a valuable second in command. That role falls to Beast, who never gets to do much with it either. Sadly Storm ends up one of the least developed characters on the show with no notable story arcs.
Toad, while being with the bad guys, and being a green, slimy, annoying brat in his first appearance, tends to have a lot of adorable, slightly pathetic woobie moments. Specifically when he's curled up on the ground whimpering while everyone else is fighting Sentinels. Or when he unintentionally unleashes the Puppy-Dog Eyes when Quicksilver refuses to break him out of jail.
Nightcrawler is a blue elf with a devil tail and long hair. This was unavoidable.
Unintentionally Unsympathetic: Cyclops. His origin episode Breakdown is meant to portray him in a sympathetic light as it recounts the misfortunes of his life, but depicting him as a lifelong clumsy, emotionally crippled man-child only succeeded in making him look worse when compared to Wolverine.
Wolverine and most of the other X-Men fall into this as well, albeit for entirely different reasons: Wolverine is unsympathetic because he's too much of a Canon Sue, while the other X-Men are too flat as characters to really sympathize with.
When Jean Grey is running around as an amnesiac in need of rescue, it's hard to feel bad for her because we don't know her very well, what little we see of her relationship with Cyclops could be seen as alternately depicting her as a Manipulative Bitch towards him, and her characterization pretty much ends at "voiced by Jennifer Hale".
When Mystique's infiltration of the school is uncovered and she is forced into retreating, the X-men just stop chasing her the moment she left the door. Despite her running into open area and the fact that they have a freaking jet, while Mystique doesn't seem to have had any escape vehicle nearby.
Talking about the X-men's front door. After an exhausting series of teleportations, Nightcrawler collapses in front of the school's front door where he is quickly abducted again by Mystique. Apparently the X-men are completely incapable of having camera surveillance on their front door and actually noticing their enemies being directly in front of it.
Marrow throwing a 10 inch long knife at a 40 feet tall robot designed to exterminate mutants. The knife just bounces of it's head and it retaliates by throwing a 10 feet long piece of metal at her, while she keeps staring in surprise at it.
Talking about Marrow; in her first appearance she scolds Xavier for not destroying Cerebro to prevent it from falling into Master Mold's hands. Cue to a few episodes later when she hands over Xavier to the sentinels in revenge, giving them exactly what they need to use Cerebro.
Cyclops is practically defined by this trope, so much so that he is literally The Load from start to finish, from flashbacks to present. You could make a drinking game out of just how many idiot moments he has.
The Woobie: while all the X-Men and even their enemies have had their ups and downs (just ask Nightcrawler) the origin episode Breakdown goes to great lengths to portray Cyclops as having had a particularly crappy life - lost his parents in a plane crash an early age, separated from his brother, stuck in a coma for two years (in this show's continuity), victim of bullying and physical abuse at the group home he was placed in, mocked and ridiculed by his first class teammates for being clumsy, nearly punked to death by Magneto, cast aside by his mentor and foster father Xavier, left to waste away in misery by the teammates who were supposedly his friends, and even having his own girlfriend Jean Grey turn against him when he got mad and sucker punched Wolverine for hitting on her (true, she got back together with him at the end, but even that was implied to be a loss rather than a gain on his part). And yet despite all of that he STILL comes across as an unsympathetic character. Granted, the X-Men often act like they don't care about him, so that's certainly not helping.
Angel easily gets it worst out of everyone present. His father parades him around to promote anti-mutant initiatives, then he falls out with his father, thenhe has his wings amputated and gets turned into Archangel. You can see his face the moment that he realises that accepting Sinister's offer was a bad idea, and it's heartbreaking.
Base Breaker: Depending on who you ask, Quentin Quire is either an entertaining breath of fresh air or an obnoxious little shit the writers are misguidedly shoving down everyone's throats.
Dork Age: Depending on who you ask, the book either only went through one during the Avengers vs. X-Men tie-ins or is one in-and-of itself.
Nausea Fuel: Snot, one of the students at the Hellfire Academy, is this incarnate. His powers are basically super-sneezing and snot that's adhesive. He can't shut it off either and apparently killed a walrus just by sneezing in its direction.
Kitty being impregnated by Brood eggs that infect her uterus. Just for the record, impregnating someone against their will? That's essentially rape, and one cover showing them all swarming around her as she's pinned down by them does not help with that.
Unintentionally Unsympathetic: Wolverine during his arguments with Cyclops whenever the two meet, but most especially in the most recent one as, while it ultimately ends with the two making peace, Logan's point is still filled with lots of hypocrisy. Generally, we're supposed to support Logan because all he wants is to keep the children safe and out of the fighting, except that he's willing to leave them ill-trained and inexperienced in doing so, thus ultimately putting them in more danger, and after AVX, he doesn't give them much choice if they want to be with him or with Scott. As well as that, we're supposed to agree with him because Logan's "supposed" to be the one who does bad and scary things, and expects everyone else to be perfect and noble and exaggerates Cyke's flaws because of this. It doesn't help that he generally acts disbarring towards Cyke's team, insulting them regularly (and he continues to do so even after Kitty has joined), and bad mouths Scott to just about anyone who'll listen. Its...pretty hard to like him when he gets like this.