Is Wolverine as the leader of the X-Men a reluctant leader burdened with The Chains of Commanding? Or has he been turned into a Drill Sergeant NastyHypocrite 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 YandereManchild, 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. For that matter, was Cyclops ever really in love with Jean or was Jean just mind-raping him the whole time? And was he ever really close to Professor Xavier, or was Xavier just mind-raping him as well?
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 at her instead of saying he's sorry (granted he does try to apologize to her later but not to Wolverine)? 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)? When Jean asked Wolverine to promise her he wouldn't get into a fight with Cyclops was it because she loved Cyclops so much that she didn't want to see him get hurt, or does she simply have so little faith in his ability to control his temper (which unfortunately appears to be justified) that she has to steer any potential rivals away from him? What was the true meaning of that little kiss she blew Wolverine in the pilot- just an apology or reaching out to her soul mate and hoping to get away from her so called "boyfriend" as soon as possible?
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?
Were Jean and Xavier using their telepathy to manipulate Cyclops into being the former's boyfriend and the latter's tin pot little soldier? Telepathic manipulation might have caused some unforeseen damage to his already fragile psyche that might have seriously messed up his emotional growth, resulting in his dysfunctional personality and behavior. It would also explain why Xavier shows absolutely no real emotional attachment or concern for Cyclops's welfare and would also explain how Jean can get away with casually showing little to no real emotional connection with him.
And the X-Men - really a family as well as superheroes, or just a barely held together group of well meaning miscreants who don't really care about each other that much, if their treatment of Cyclops is anything to go by?
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.
Wolverine, as usual. The focus on him and Character Shilling is taken to almost parody levels; is it right to focus on the character who's already the most popular X-Man, or is making a Canon Sue out of him ruining him and the series? Also, the Character Shilling sometimes not being backed up by his actions can also either mean that he sucks, or that he's not a Canon Sue and still the Wolverine of the comics.
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.
The cause of this particular broken base is almost certainly the flashbacks of Cyclops. Before that, he was shown to be a broken man who was understandably grief stricken over the violent disappearance (and possible death) of his long time girlfriend, but everyone talked about how in the old days he held the team together. But from the flashbacks, we see that he was always a loser. From day 1, he was never the responsible, respected leader of the X-Men. So instead of being the leader who collapsed after the loss of Jean, he was the loser who somehow managed to snag a hot chick, then attacked anyone who even looked at her, and reverted to his loser status the moment she was gone.
Broken Base: The entire series had this going on among comic fans. Some believe it to be the best, most pure and most spiritually honest X-Men series ever, others felt it was just another lame Wolverine cash grab loaded with mostly flat, unlikable characters and mediocre writing.
Although, people who hate the show do have a point. For a show that was supposed to be all different and edgy and unlike any X-Men cartoon ever seen before before...the series recycled lot of familiar beats 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 comics and other versions.
The Shadow King, real name Amahl Farouk, from "Overflow," is a cruel and merciless telepathic mutant who forced the young 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.
Sebastian Shaw, from the final 4 episodes, and Selene (Gallio), from the final 2 episodes, are the leaders of the Inner Circle, a group dedicated to destroying the Phoenix Force, a potentially destructive cosmic entity, in order to save humanity. They send Emma Frost and her students, the Stepford Cuckoos, to Xavier's school to incapacitate Xavier and capture Jean Grey. Their psychic attack causes the Phoenix Force to go nuts and blow up the school, putting Xavier into a coma and giving Jean amnesia for most of the series. Emma tricks the X-Men into letting her join. At first she is just a spy, but she soon grows to care about the X-Men. The X-Men eventually find Jean, but Emma knocks them out and delivers Jean to the Inner Circle. However Shaw and Selene reveal they do not plan to destroy the Phoenix, but harvest its power for their own selfish purposes, endangering the whole planet just to satisfy their power lust. They plan to trick Jean into releasing the Phoenix Force and then having the Stepford Cuckoos absorb it, endangering their lives in the process. Selene also reveals to Cyclops that Emma was responsible for the explosion at the school, just to rub salt in Emma's wounds. After the Stepford Cuckoos absorb the Phoenix Force, Shaw orders them to kill all the X-Men and burn Genosha to the ground. Their actions lead to the Phoenix Force destroying most of humanity and setting up the Bad Future Xavier finds himself in, when he wakes up.
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.
However, these problems were just difficulties in character arc as a whole due to the fact that whenever he is supporting character, Cyclops is usually pretty competent and likable. The episode "Overflow" portrays Cyclops getting over himself to go help the team save Storm. To his credit, he was one of only two X-Men in that episode who actually got to help Wolverine stop Storm from flooding Africa. Another example of this is in the episode "Backlash", which gives us a glimmer of Cyclops acting more like his comic book counterpart and most versions. When Quicksilver wanted the Brotherhood and X-Men to run and abandon Wolverine, it is Cyclops who convinces him to stay and states they're going to stay there and buy Wolverine time that he needs. Cyclops even briefly took command of the situation through issuing sound orders, like getting Quicksilver to use his super speed to draw way the Sentinels fire so the group could recover. The problem was whenever episode focused on him they focused on the obsession that he had with Jean.
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 in the back for nothing more than a petty jab 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?.
Draco in Leather Pants: Emma seems to get this. While she has sympathetic qualities, fans tend to ignore every immoral action she commits, and in fact, Jean's reaction to one of them, kissing Scott while he's out cold, is frequently brought up as a reason to hate Jean.
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.
Ho Yay: As per usual, Cyclops and Wolverine fight and bicker like an old married couple.
And, as usual, Magneto and Xavier, what with how Magneto puts time aside to keep Charles alive on Genosha and a not so subtly flirty moment between them in the flashbacks of Breakdown.
Mr. Sinister was rather flirty with Angel when he pitched him his idea for turning him into Archangel.
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.
It's the Same, Now It Sucks: The animation and character designs, while not terrible, are nothing special. While the previous X-Men animated adaptations managed to give everyone their own unique and distinct look, WATXM's designs are all pretty much identical to the other animated versions 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.
Jerkass Woobie: Cyclops is meant to be this, but unfortunately he ends up being more Jerkass than Woobie.
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.
Magneto in the "Foresight" three-parter. In the prior episode, Wolverine and Xavier showed him and Senator Kelly what'll happen if they go to war. Kelly took the Bad Future to heart and changed course, but Magneto saw an opportunity. He had Quicksilver kidnap Kelly and Mystique replace him in order to initiate the war. His reasoning is that controlling the other side of the fight meant he could avert the worst outcome for his own, but in order to truly sell mutants on the idea that Humans Are Bastards, he was going to allow those on Genosha to be massacred by Sentinels. You can see why Scarlet Witch and Polaris ultimately exiled him from Genosha.
Jean yelling "Scott! What are you doing?! It'll kill you!" when Cyclops tries to fight the Phoenix in the final episode "Foresight: Part 3" 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.
Jean throwing Emma up against a wall with telekinesis, binding her there with pipes, coldly saying "You'll pay for what you've done." It's supposed to be chilling, but Jennifer Hale gives such a flat reading that the threat means nothing, and the "angry" expression on Jean's face is just silly.
Pretty much any scene where Cyclops yells, due mostly to the normally reliable 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.
Xavier's "You Must Lead Them Logan..." spiel.
There is also the fact that an entire episode revolved around the X-Men being too dumb to fend off a bunch of rinky-dink ninjas.
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.
What little is shown of Cyclops and Jean's relationship and the former's obsession with finding the latter is Narm at best, and at worst a clearly dysfunctional and unhealthy union built on insecurity and neediness instead of affection, respect, trust, in other words, all the things that actually make a truly loving relationship work. This makes it next to impossible to actually root for Cyclops to find Jean since their relationship doesn't work all that well based on what little is actually shown. Whether this was intentional on the part of the writers in order to make Emma look like a better girlfriend for Cyclops than Jean or simply a result of bad, sloppy writing is anyone's guess.
Furthermore, the show's writers really backed themselves into a corner with how they characterized Cyclops as this insanely pathetic Manchild. At best they made Cyclops look weak, stupid, foolish and clumsy, and at worst they made him look like a budding psychopath with serious anger management issues - and that was BEFORE he lost Jean, so the problem here is that there's absolutely no good reason for Jean to have ever fallen in love with him, let alone like him; as near as anyone can tell she apparently only tolerated him because he worshiped the ground she walked on. Likewise, the show never offers a genuinely good reason for why Cyclops ever fell for Jean other than she saved him from Magneto and a weak, half assed line about her taking "the pain away". This only serves to make Cyclops's quest to find Jean look even more ridiculous, and ultimately neither character comes away looking particularly good for it.
Ron the Death Eater: Hoo, boy, does Jean Grey get no end of this. It seems there's a not a single action the fans haven't demonized her for, and ironically, all of them are either pretty understandable, or just plain harmless. Jean engages in a bit of telepathic flirtation? She's obviously brainwashing Cyke. She gets ticked when her boyfriend blasts a (very heavy) man in the back, hard enough to knock him to the ground? She needs to lighten up! She ties down a woman who was presently *assaulting* her boyfriend? That psycho! She was just getting a taste of her own medicine! Serves her right!.
The problem is Jean has very little screen time and she has no characterization beyond simply being voiced by Jennifer Hale, so it's easy to have a negative view of her and/or her relationship with Cyclops in this series, especially not when it seemed early on that the writers were deliberately setting her up to look like a bitch in order to make her rival Emma Frost look better by comparison (which undermines the integrity of trying to make Cyclops's determination to find her feel like a viable subplot). Perhaps it is understandable for her to be upset that he lost his temper and took a cheap shot at Wolverine, but she's known Cyclops long enough by this point to know that he has some serious anger management problems, which brings up the question of why she continues to be in a relationship with him when his anger obviously bothers her. It's not exactly healthy to be in a relationship with such an emotionally unstable man, and yet a supposedly sane woman like Jean has been with such a man for years despite this, and it looks progressively worse because the series does not give Cyclops any positive traits to justify Jean still being with him after such a long time. As for no evidence to support the theory that Jean used her telepathy to brainwash Cyclops into being her boy toy, well, maybe not obvious evidence, but we've seen telepaths casually Mind Rape people before into giving them what they want, Jean's own mentor Professor Xavier himself was shown to do this in the comics, and for all we know when she was still a teenager Jean might have used her powers to make Cyclops fall for her without Jean herself even realizing it. Also, going by those flashbacks, Cyclops was clearly a mess when he met her, and she was presumably doing only a little better than him, she probably sensed right away what kind of boy he was, and she almost looks amused by it, and then proceeds to choose him over more emotionally stable and competent members Angel and Beast, which looks incredibly suspicious that such a powerful young lady would choose a clumsy, emotionally crippled boy other than pity or just wanting someone she could string along. The simple fact that they officially hooked up after Jean basically rescued Cyclops from Magneto really does make it look like she was taking advantage of him, with Jean putting the visor back on Cyclops's face (instead of just letting him do that himself) practically symbolizing her control over him. At any rate, there's no denying that the relationship between them is incredibly dysfunctional and unhealthy, and while Cyclops is undeniably the one who comes away looking far worse for it, Jean violently binding Emma to a wall with pipes for kissing Cyclops does make her look incredibly clingy and possessive towards him (and Emma never even had a chance to do half the things she got away with in Grant Morrison's New X-Men comic). The chances of their relationship being salvaged into something respectable in the abandoned season 2 were highly unlikely.
Rooting for the Empire: With Wolverine in full on Canon Sue mode, Cyclops as an unsympathetic Jerkass psychopath, Xavier as 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.
Straw Loser: 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.
They Changed It, Now It Sucks: Good Lord! A lot of fans were not happy about Cyclops and Wolverine's role swap, nor did the fact that Wolverine was the leader of the X-Men instead of Cyclops.
The fact that Storm was demoted to an background character did not sit well with fans, nor did the fact that Professor Xavier and Jean Grey were reduced to plot devices.
Many fans absolutely despised this version of Cyclops for not being portrayed as the Standardized Leader that he usually is portrayed as in the comics and most versions.
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.
However, Cyclops' flaws in WATXM are just difficulties in character arc as a whole due to the fact that whenever he is supporting character, Cyclops is usually pretty competent and likable. The episode "Overflow" portrays Cyclops getting over himself to go help the team save Storm. To his credit, he was one of only two X-Men in that episode who actually got to help Wolverine stop Storm from flooding Africa. Another example of this is presented towards the end of the episode "Backlash", which gives us a glimmer of Cyclops acting more like his comic book counterpart and most versions. When Quicksilver wanted the Brotherhood and X-Men to run and abandon Wolverine, it is Cyclops who convinces him to stay. He states they're going to stay there and buy Wolverine time that he needs. He even briefly took command of the situation through issuing sound orders, like getting Quicksilver to use his super speed to draw way the Sentinels fire so the group could recover. The problem was whenever episode focused on him, the writers focused on the obsession that he with Jean.
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 and no real reason to be there at all. They Wasted a Perfectly Good Character indeed.
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.
Unfortunate Implications: Cyclops's entire characterization and subplot in this series is one big case study of unfortunate implications mainly due to the fact that it obviously has the purpose of presenting Wolverine as a better hero and a suited leader of the X-Men. Cyclops' flashbacks portray him as clumsy and stupid instead of the competent, hard working student from the comics and most versions whose primary weakness was a lack of social skills and he was seemingly incapable of doing anything right before Jean came along (he couldn't even do something as simple as blasting Magneto at point blank range), became violently possessive and needy about her when challenged for her by Wolverine, and was incapable of moving on from losing her, despite the fact that Jean didn't seem to really even like him that much, even though he had the lovely anti-Wolverine Emma Frost right there in front of him the whole time. And on top of all that, he got punked by a bunch of stupid ninjas. Even if a second season had been made that supposedly portrayed him in a better light (when not showing him as a villain in the future) there would have always been that nagging feeling that Cyclops wasn't truly performing feats of heroism on his own but was merely acting as a kind of offshoot of Jean Grey's superiority.
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 a jerk and 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".
Emma Frost, supposedly seen as a tragic anti-villain, loses quite a few sympathy points when she effectively assaults an unconscious Cyclops.
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.
His actions with Wolverine were particularly idiotic. Wolverine's getting a little too cozy with his girl, and he makes some not-too-subtle remarks about his worthiness. Instead of making some remarks of his own like pretty much every other version of the character has done, or suggesting they fight it out, he shoots him in the back, full blast, predictably pissing off Jean, and making Wolverine respect him even less with his cowardly attack.
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 - (presumably) 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-Breaking Character: 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.