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  • Alternative Character Interpretation:
    • The Brotherhood. They're an Ineffectual Sympathetic Villain team, but does that mean they're bad people who are just too pathetic to be a serious threat, or are they actually misunderstood misfits who never got a chance?
      • By extension, its shown that Xavier would gladly welcome them if they wanted to join, but did he try hard enough to reach out to them, or did he leave them to their own devices so as to not have to worry about the difficulties they'd bring?
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    • Lance in particular: Did he really have a heroic side, or was he solely motivated by trying to get Kitty to like him? Can it be both in the end, with Lance starting to do good things just to get Kitty into liking him, but ultimately developed into a better man because of it? In this case, is it Love Redeems, or is Lance just turning Kitty into a prize for him to 'win' by being good?
    • Scott: Was he just trying to be a responsible though imperfect leader, or just a full-on Jerkass?
    • Were the New Recruits complete idiots who crossed into Too Dumb to Live, or just inexperienced and excited at the prospect of being mutants that they got ahead of themselves a few times?
      • More specifically, Bobby/Iceman. Did he truly learn his lesson and become a good asset to the X-Men/New Mutants, or were his Too Dumb to Live credential just swept under the rug?
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    • Was Spyke an asshole who was Easily Forgiven only for being a newbie and Storm's relative, or just an budding antihero who was too young and constrained to do it right?
    • Did Mystique really try to help her stepdaughter, or was it just her way of emotionally manipulating her to get more information easier? And what about her and her biological son Kurt...?
    • All of Magneto's actions with Wanda. Given how powerful Wanda is, her lack of control is indeed something to fear. Having Mastermind Mind Rape her could've been more of a last resort since he did try to resolve things the old fashioned way beforehand. Of course, then there's the question of how much he regretted the act.
  • Accidental Innuendo: A lot of Lance's dialog comes off as this because of all his rock puns. Season 2 Episode 1 had these lines by Lance & Kitty:
    Kitty: Shouldn't you be erupting Somewhere?
    Lance: Hey Kitty, you wanna see some real shaking?
    • Scott's Badass Boast of "You want it raw? Then take it raw" takes on another meaning with modern gay terminology.
  • Anti-Climax: Apocalypse's final defeat in the Grand Finale. Despite all the buildup to how powerful he is (taking out Magneto, Mystique, Xavier, and Storm and converting them into his Horsemen), Apocalypse is Hoist by His Own Petard and foiled by Wolverine and Rogue (the same mutant he manipulated). While the irony of him being defeated by his own pawn is not lost, the fact that it was only herself and Logan and not, say, the entire X-Men/Brotherhood alliance dials down Apocalypse's gravitas. Justified, however, in that the alliance was spread all over the globe dealing with Apocalypse's pyramids and Horsemen, and when they did arrive at Apocalypse's Egypt lair, he was already defeated.
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  • Arc Fatigue: Season 2 has very few ongoing story arcs, and due to the fairly standalone nature, drags on without anything particularly interesting happening until the finale episodes, where mutants are outed to the world.
  • Author's Saving Throw:
    • One of Season 3's arcs culminates in Spyke, the least popular member of the main team, leaving to join the Morlocks due to his mutation growing out of control. While he did return later, he was considerably reworked in such a way that made him a much more interesting character.
    • Given the Broken Base nature of the couple, Lance returning to being a hostile anti-villain and Kitty dumping him in season 3 could be seen as this to some. Them seemingly getting back together in the finale, or at least implied, would be this for others.
  • Base-Breaking Character:
    • Avalanche. Due to Characterization Marches On, he went from being a volatile Jerkass with a Hair-Trigger Temper and a shade of Manipulative Bastard in his debut episode who nearly killed Kitty and her parents to spending season 2 as a love-sick, but hot-headed, Nice Guy chasing Kitty, and by the last season settles on being an Jerk with a Heart of Gold Anti-Villain. Some adored him as a result and found his relationship with Kitty to be sweet, while others thought it was forced and thought he came off as a creep (not helped by how some scenes indicated he didn't care for Kitty's consent).
    • Jean. To some extent there's a great degree of Vindicated by History; for years she was written off as an annoying Damsel Scrappy with a Holier Than Thou attitude, but a lot of this came from Brotherhood and Scogue fans, and some of the things she was hated for were very much a case of Double Standard. Long after the fact though, many modern X-Men fans who adore Jean Grey cite this show's version as being one of their favourite takes on her.
    • The New Recruits, especially Iceman, got a lot of hate for their idiocy, while others enjoyed it and found them hilarious. "Joyride" is generally cited as an example of them going too far, though.
  • Best Known for the Fanservice:
    • If not for the reasons detailed below, "Walk on the Wild Side" is remembered for the X-girls and Boom Boom donning sexy black leather outfits to fight crime.
    • "Spykecam", the episode where Sabretooth first appears, is better remembered for Rogue and Kitty's dance after Rogue absorbs a bit of her skills. While the show was always well-animated, this got an Animation Bump (and was modeled after a similar dance in Buffy the Vampire Slayer), making for some very smooth and sensual dance moves.
  • Big-Lipped Alligator Moment: The completely out of nowhere music montage in "Walk on the Wild Side".
  • Bizarro Episode:
    • Said episode, "Walk On The Wild Side", counts for some people - it comes off as an Anvilicious "feminism" episode that has just gotten worse with age, but since it's filler, people who dislike it tend to simply ignore its presence.
    • "African Storm", since the episode is about a shaman from Storm's tribe stealing her soul, when magic is only mentioned a handful of times throughout the entire series. Sadly, this is the only episode where Storm is the main focus.
    • Another episode had Forge's research into how Nightcrawler's teleportation works accidentally release demonic-looking monsters from some kind of Hell dimension.
  • Crazy Awesome: Everything the New Mutants do. Hilarity Ensues was pretty much their MO.
  • Contested Sequel: While not an actual sequel series, it's got a fair amount of dislike from those who grew up with X-Men, but some others liked this incarnation just fine, if not prefer it. Critics attack the show for its lack of fidelity to the source material, its de-aging of all the mutants to teenage and YA versions of themselves, and toning down of violence. Defenders point out that it's the only animated incarnation of the X-Men that isn't bogged down by Wolverine Publicity (the showrunners made it a point of making only one or two Wolverine-centric episodes per season), it also allows proper space and room for an ensemble cast of mutants, where the relationships don't take attention away from the socio-political metaphor and by introducing X-23, it produced a highly successful Canon Foreigner who was ultimately adapted into Logan, the most critically acclaimed and commercially successful of all the entries in the X-Men Film Series, and as such one can argue that Evolution made a more lasting contribution than the original Fox adaptation did.
  • Die for Our Ship:
    • The Nightcrawler/Shadowcat fans had a bad tendency to do this to Amanda and Lance. Amanda would usually have her canon-characterisation inverted where she was suddenly ashamed of Kurt's appearance, when in the show she was often too encouraging and wanted him to be proud of how he looks. Lance meanwhile would be given a massively exaggerated take on his season 1 characterisation, to the point he became a full on rapist in some works. In this case, it seems fans would latch onto brief moments where he's shown grabbing Kitty's arm possessively and dialled up until he was a full on abuser.
    • Jean was bashed by Cyclops with Rogue fans pretty much constantly, where she'd be turned into a full-on Alpha Bitch to give the more relatable Rogue a reason to fight for Scott. Scott and Jean also got this a lot from Gambit/Rogue fans, seemingly just to make Gambit and Rogue's relationship seem cooler by comparison.
  • Draco in Leather Pants:
    • The Brotherhood, as a result of how they became completely ineffective as threats and descended into borderline Friendly Enemies with the X-Men during season 2, often get turned into well-meaning misfits who's only crimes are the result of being manipulated by Mystique and Magneto, while ignoring how they were all serious criminals before those two recruited them and even when on their own, could get into serious trouble and cause massive amounts of damage.
      • Lance and Pietro get this the most (though, for Lance this was canon in the second season), with Lance becoming nothing but a sweet and caring boyfriend who's perfect for Kitty, while his temper and antagonism towards the X-Men (which was almost always instigated by himself first) that he demonstrates throughout the rest of the series is downplayed completely. Pietro meanwhile is often turned into a Loveable Rogue at worst in fanworks and romanticised greatly for OC characters to fall in love with. Ironically, Pietro was heroic in the comics, but the show version gave him serious Adaptational Villainy, and while you'd expect this to be a case of people applying the comics canon to the show version, generally it was people who didn't follow the comics who did this.
  • Ensemble Dark Horse:
    • The Brotherhood started out as stock villains for the X-Men to battle in the first season, but became incredibly popular. This likely led to their roles as Anti Villains and eventual Heel–Face Turn.
    • Gambit proved very popular despite only appearing in a handful of episodes.
    • The New Recruits, particularly Bobby, Sam, Jubilee, Ray, Amara, and Jamie were all beloved by some vocal segments of the fans.
  • Epileptic Trees:
    • While Ray started out as a Morlock in the comics, the writers never clarified just what his connection with them was in the cartoon, other than the fact they were both mutually familiar with one-another. And the implications of that connection has made his back story even more ambiguous, even compared to the other Recruits, given that most of them never discussed their backgrounds. Most of the fans tend to write him, in fan fiction, as the child of a broken home who ran away and wound up with the Morlocks before being found by Professor X. They also tend to explain that the Morlocks actually pretended not to know him, since he left them they saw it as an act of betrayal and have since shunned him.
    • People on The Other Wiki have made some guesses about Avalanche. Namely, they've guessed he's likely Greek, with 'Alvers' being an Americanized corruption of the name 'Alvez', and that his middle name is 'Domonic' to match his name in the comics.
  • Evil Is Cool: The Brotherhood, though this is more like "misbehaving yet not being super evil is cool".
  • Evil Is Sexy:
    • Mystique, naturally.
    • The Brotherhood in general have fangirls who find them extremely attractive, except for Blob, but like before, more "Criminal misbehavior is sexy than evil is sexy". (Unless it's Tabitha, yeah.)
    • Likely a large part of Gambit's appeal, though he's technically not evil, so much as he doesn't really care about anything besides himself and his pockets though he still has a heart of gold, deep down.
  • Fanon Discontinuity: "Walk on the Wild Side" gets a considerable amount of hate from fans due to being an incredible ham-fisted "girl power" episode that has multiple characters, most glaringly Scott, acting out of character to shove the message down the audience's throat. Mind you, this show NEVER treated the female characters as less than the males. The tone and characterization are so alien to what the show normally is the episode itself is a borderline Bizarro Episode.
  • Fandom Rivalry: Many fans of the previous cartoon do not take kindly to a comparison between the two, especially ones favoring Evolution.
  • Fan-Preferred Couple:
    • Rogue and Gambit ended up being the most popular couple, mostly due to their comic book counterparts, eventually leading to the creators devoting an episode to setting them up (and the final scene implying they were together).
    • Cyclops and Rogue actually became a MAJOR contender from this series, to the point where most of the creators working on it had to be reminded to give Jean more sympathetic character development to make her eventual coupling with Scott more acceptable. Even so, series creator Frank Puar made no secret of the fact that had the show continued into future seasons, Scott and Rogue would eventually become a couple following Jean having a lethal encounter with the Phoenix.
    • Nightcrawler/Shadowcat. It was mostly a side-effect of porting their relationship from the comics to the show. Kurt's canon crush on Kitty prior to dating Amanda and their consistently close friendship after probably helped, along with them being the biggest Ship Launchers in the fandom.
    • Storm and Wolverine are an odd case as they did have a few genuine Ship Tease moments, fans just wanted way more of it.
  • Foe Yay:
    • The show seemed to set up a few of the X-Men and Brotherhood as having counterparts on the other side. Avalanche with Cyclops wrote itself with their rivalry. The same can be said with Toad with Nightcrawler and Spyke Quicksilver.
    • Magneto with Xavier! Those to have so much Unresolved Sexual Tension between them it isn't funny. There was the suggestive looks, the fact that Magneto protects him at several points in the series and Xavier's unfailing objections to putting an end to Eric. This can cross to Ho Yay when Magneto does a Heel–Face Turn (or in the origin when they were still on the same side).
    • Wolverine x Mystique. Pretty much all the banter they have, especially in "The Cauldron, Part 2", makes them seem Like an Old Married Couple. The fact that they sit next to each other on the XM Velocity adds to this.
  • "Funny Aneurysm" Moment: In Wanda's first extended appearance in "The Hex Factor" (when she goes berserk and tries to attack Pietro on sight), Toad half-jokingly asks Pietro if she's his ex-girlfriend. Four years after that episode came out, Mark Millar and Jeph Loeb rather infamously wrote Wanda and Pietro as an incestuous couple in The Ultimates, much to the consternation of many fans.
  • Growing the Beard: The show has decent to average quality in season 1. Near the end of season 2 and the beginning of season 3, however, the show becomes more serious, while still retaining its playful humor, and focuses more on characterization and action. Seasons 1 and 2 focused more on introductions and romance respectively.
  • Hilarious in Hindsight:
    • It's a bit ironic that Noel Fisher would voice Toad, a mutant resembling a frog-human hybrid, considering that one of his earlier roles was Troy McGinty, who was deathly afraid of a human-frog hybrid children's show character named MacGoogles. He'd also go on to play a very different kind of mutant.
    • Apocalypse turned Storm, Prof. X, Magneto and Mystique into his Four Horsemen. Storm and Magneto will be two of the Four Horsemen in the movie X-Men: Apocalypse (the other two will be Angel and Psylocke).
    • In "The Cauldron, Part 1", Storm fights Mystique, saying she doesn't care why she chose to attack her, before knocking her out. In X-Men: Apocalypse, Storm says that she idolizes Mystique.
    • The Brotherhood watching the Powerpuff Girls in "Dark Horizon" ends up a bit funny as a majority of the cast from the show ended up working on Demashita! Powerpuff Girls Z later on.
    • David Haller/Legion appears in one episode, with more realistic short blonde hair instead of his infamous look from the comics. Years later, his only other on-screen appearance also went with short blonde hair.
    • The episode "Spyke Cam" has Spike get a B on a test over the The Star Wars Program because he confuses it with the film it was named after. Much later, Disney would end up buying both Marvel and Lucasfilm to bring both properties under the same roof, making the joke even more humorous.
    • The Season 2 episode "Power Surge" makes a throwaway reference to pineapple over pizza in 2001, which was long before debates over the topping would take the Internet by storm.
  • Ho Yay:
    • Yaoi fans were particularly interested in what Avalanche and Quicksilver did with their free time together living in the Brotherhood Boarding House.
    • Nightcrawler and Cyclops:
      • In "SpykeCam", Evan says, "Scott's pretty stiff, but Kurt usually takes care of that." Can't make this up.
      • The scene where, after the mansion is destroyed and characters have to share rooms, Scott and Kurt emerge from their bedroom with Scott being covered in Kurt's fur.
      • In "Walk on the Wild Side" Scott at one point grabs Kurt and tells him to cancel his plans for the night with a mischievous look, without context it has some heavy homoerotic connotations, something fans were quick to pick up on looking back at it.
    • And Wolverine and Captain America in the season 2 episode "Operation Rebirth".
    • The entire "Bayville Sirens" montage in "Walk on the Wild Side". Especially the part where Jean and Magma are grinding on each other.
    • Amara. Tabitha. That's all.
    • Risty asked Rogue to a Sadie Hawkins dance. That is literally what happened; Scott was taken, so Risty suggested that she and Rogue go. This, of course, makes the reveal that Risty was Mystique this whole time VERY awkward.
    • Storm's fight with Mystique in "The Cauldron, Part 1" is Orgasmic Combat at its finest. Not only is there a lot of tackling, embracing, and other forms of intimate contact between the two, but the fight is accompanied by large amounts of rough grunting and panting, and when Storm finally knocks Mystique unconscious, they both audibly climax at the same time.
  • Idiot Plot: Say what you want about most of the episode, but "Joyride" falls apart pretty quickly when you remember Wolverine's advanced senses and Xavier and Jean's telepathy, either of which should have identified who was the culprit instantly.
  • Jerkass Woobie:
    • Evan evolved into this. While he was probably the X-Men's most Jerkass member, he developed into a Woobie during Season Three after anti-mutant sentiment caused former friends to start bullying him. While they were all suffering, Evan was the only one to be shown repeatedly being picked on for his powers, all the while also slowly but steadily losing control of his very visible powers. Eventually, he takes a Mutant harming poison (which were supposed to be a toxin eliminators) and completely loses the hang of his abilities, so the poor kid moves in with the Morlocks as, despite the X-Men's good intentions, the Morlocks are the only ones who can understand his pain. And worse, its unconfirmed if they stop being poisoned by Power8 or if the effects will ever wear off, and they never mentioned if there was a cure.
    • A big reason why the Brotherhood were so popular, and what fuels a lot of their Draco in Leather Pants, Die for Our Ship, Rooting for the Empire fans. They're all criminals even before being recruited, but they're also all basically without any real parental supervision and essentially live in poverty due to none of them having a source of income. To a lot of people, this makes their criminal behaviour and antagonism sympathetic.
  • Launcher of a Thousand Ships:
    • Both Kitty and Kurt are beloved by shippers. It likely stems from their popularity, or their easiness to relate to, but Kitty's pretty much shipped with every guy in the series, and Kurt's shipped with everyone, everyone. You would think save for Rogue, but nope, he's shipped with Rogue, too. Never underestimate fanfic.
    • The Brotherhood also seem to end up with everyone. Well at least Lance, Pietro, and Toad. The Blob aka Fred Dukes, doesn't exist in fanfics.
  • Memetic Mutation:
    • I WILL CRUSH YOU LIKE A CAANN!!
    • "Chicks dig the fuzzy dude!"
  • Moral Event Horizon:
    • Pietro had his when he had a train derailed for the purpose of pretending to save people, and upon finding out that if they fail hundreds will die, including himself, he runs away and leaves those trapped, and potentially the entire town, to die.
    • Toad stole Kurt's image inducer — not that bad, until you remember that he purposely chose to do it while Kurt was meeting with his girlfriend Amanda's parents, ruining his chance at making them like him.
    • Magneto almost crossed this when he has his own daughter Wanda mindraped, replacing her memories of him abandoning her in a mental institution, which is what made her become a Dark Magical Girl in the first place, into loving memories that made her forget his abuse. However, it's tempered by the fact that he asked her one last time if they could start over (meaning she wouldn't try to kill him anymore), and she adamantly refused. It's when he says that "hopefully your mind won't be too damaged by the process" without a hint of regret or pain in his voice that he runs over the line with a truck.
    • If Mystique didn't cross it when she replaced Xavier and tried to kill the New Recruits, for no reason other than them being unable to fight Magneto, then she did it when she kidnapped Scott, stealing his Power Limiter ruby quartz glasses, and leaving him stranded in the middle of nowhere, repeatedly attacking him and eventually trying to kill him while he's unable to see. All to get back at him for leaving her behind when she refused to tell them where she imprisoned Xavier.
    • Duncan Matthews and his pals went from Jerk Jocks, to repeatedly physically assaulting Scott unprovoked after he was outted as a mutant, to post-graduation attempted mutant murder with mining machinery and munitions. That last one got them locked up in prison though. Duh.
    • There was also the soft-drink manufacturer who unknowingly laced his drink with mutant poison. You can tell he's genuinely surprised... then Mood Whiplash kicks in and he figures he can make a lot of money off the discovery. It ended up not going anywhere, however.
    • Apocalypse was planning on using his machine to turn the populace into mutants... But even he notes that this may kill much of the human population, due to their bodies not being able to take it. He still was willing to go through it.
    • Principal Kelly went from being a possibly bigoted jerk of a principal to a complete bastard when he starts encouraging bullying of mutants and has both the Brotherhood and Duncan team-up to attack Scott so he can convince the school board that mutants are violent and dangerous.
  • Narm:
    • Wanda's flashback to when her father carted her off to a mental institution might have been more emotionally effective if they didn't use the exact same voice clip of her crying out to her father three times in the flashback, with those being her only lines aside from "Don't leave me...".
    • When Professor X is revealed to be Mystique in disguise, the drama of her line "things are about to get much worse" is ruined when there's a pan of everyone else making scared faces that just look goofy.
  • Never Live It Down:
    • Scott was a bit of a stick-in-the-mud but was overall a decent guy. However, "Joyride", where his rivalry with Lance was played up to give Lance an antagonist as he tries to join the X-Men, and as a result Scott became the biggest punching bag for Brotherhood fans. Ironically, he actually made a lot of good points against Lance's membership and did try to be friendly, until Lance's disrespect pushed him into retaliate, but people ignore this and focus solely on how he turned the Danger Room machine on to humiliate Lance in front of others.
    • Similarly, the New Recruits are only remembered by some fans as Too Dumb to Live assholes, thanks to the same episode. Even though their learn their lesson after, some blame them entirely for Lance quitting since they willingly allowed him to take the blame for their stunts, and as a result some seem to think they were only ever shown as incompetent dumbasses.
  • Nightmare Fuel:
    • Mesmero's introductory episode was this from the beginning to the end in episode 25 (Mindbender). There was no blood, no ultra violence, no huge fights... just him kidnapping and brainwashing a bunch of innocent kids ( Jean, Kitty, Evan and Kurt), using them to set off his Evil Plan to wake up his master Apocalypse and slipping unnoticed under their caretakers' watch. And he starts this by entering the kids's dreams and turning them into nightmares. Poor, poor Jean Grey. Watch it here, with the Latin-american dub conveying the feeling almost as well as the original...
    • Blind Alley wasn't much better. Scott gets stranded in a deserted town as Mystique's revenge for him derailing her Evil Plan without his visor, completely unable to even open his eyes or he'll blast everything on sight into nothingness...
    • Apocalypse straddled the line, helped by the fact he wasn't particularly wordy in this continuity.
  • Rescued from the Scrappy Heap:
    • Spyke, who after living with the Morlocks, became a powerful, mutant-protecting vigilante that can light his spikes on fire.
    • Jubilee is often regarded as the most useless X-Woman to the general public (comic audiences feel differently though), here however, she's an Ensemble Dark Horse.
  • Romantic Plot Tumor: Brotherhood fans and Scogue fans consider Scott and Jean's relationship this, as to be expected given how often they received Ron the Death Eater treatment from them. It took three seasons of them developing from close friends into a committed couple, so for those wanting to see Brotherhood hijinks or those that wanted Scott with Rogue, their time together is a chore.
  • Ron the Death Eater:
    • The Brotherhood fandom in general was known for this, primarily towards Jean and Scott. To go into detail:
      • In canon, Jean was easily the friendliest character in the show. Somehow, to some there's a perception she was too perfect and lacked any flaws while at the same time thought she was a horrible Alpha Bitch, despite the two being completely contradictory. Though primarily by Brotherhood fans, this was also used by Scogue shippers so they could free Scott to be with Rogue.
      • Scott was a workaholic with little sense of humour and quite the hot-head, but he was also a very protective Big Brother Mentor to the rest of the team, apologised every time he was out of line, and for the most part was one of the most heroic and well-intentioned characters in the show. Because he was the one with the most personal dislike towards the Brotherhood though, he's often presented as a massive Jerkass who only serves as to be in the way of their fun rebellious nature or possibly give any potential rival for Rogue's affection someone to fight against. A lot of it also comes from how his character suffers this in the comics fandom too, with many of the commonly-cited events that are usually thrown at him being brought up by those that are giving him shit.
    • Conversely, Lance/Avalance. He was an villain, but some tend to ignore how his relationship with Kitty was presented to instead twist him into a rapist and/or abusive boyfriend towards Kitty. Even when he was being a Jerkass he was never that bad, and even the times he was toxic towards Kitty pale compared to how fandom sometimes treated him.
    • Magneto is an odd case of this as he's a villain, and the Big Bad of Season 1, but despite that, some fans seem to miss the part about him being an Anti-Villain. While what he did to Wanda was horrible parenting, a lot of fans, especially Brotherhood fans, act like he was outright physically abusive towards Pietro, while he's given a serious case of the opposite trope with them acting like he was always disgusted and opposed by how Magneto treated her (the neglect and the brainwashing), despite him being seemingly supportive of both. Magneto is often treated like a monster just to justify some of Pietro's bad behaviour, and seemingly ignore the pseudo Heel–Face Turn he took mid-Season 3 to take on Apocalypse.
  • Rooting for the Empire: The original Brotherhood members just don't come off as evil to many fans, despite all the horrendous things they did including rigging a train accident to look like heroes one last time and then fleeing when they discover it's going right at another speeding train with eight tankers of fuel. Even with this, however, they spent so much time when in the spotlight being more Chaotic Neutral than outright villainous that many took a shine to them and thought that they'd be far more fun to hang out with.
  • The Scrappy:
    • Spyke was an example of the crew's attempts to bring in a brand new X-Men character for the series who would be the "epitome of cool." This failed so badly (with almost all of the fans being irritated by his "cool lingo"note , overall skater persona, and being kind of a jerk who often forgot the lessons taught to him). Though he got seriously Rescued from the Scrappy Heap over time, generally in the popular census, if anyone brings up his character, its usually to say what a lame character he was.
    • Boom-Boom when she first joined The Brotherhood. Strangely, despite the fact that Tabby was fairly abusive towards the Brotherhood boys, and had little to no respect for their personal space or feelings, often stealing from or pranking them, a lot of fans don't focus on this. Rather, they focus on her flirting with boys quite a bit as the reason to hate her.
  • Seasonal Rot: To some, Season 2 is this, due to its over-focus on romantic side plots, less focus on their battles and less action, though the ending managed to fix that by revealing The Masquerade, leading to it Growing the Beard in Season 3.
  • Slow-Paced Beginning: The first two seasons of the series are mostly episodic, introduces what could be considered too many characters, and drag on for quite a while. But upon the Season 2 finale, and the beginning of Season 3, the series begins putting emphasis on much longer story arcs, and the core themes of discrimination that the franchise is known for.
  • Strangled by the Red String: Liked or not, Kitty/Lance pretty much came out of nowhere. Season 1 had no indication there was any attraction between them, but in season 2 Lance suddenly has a crush on her which she starts to reciprocate shortly after. There was a Deleted Scene where he saved her from some falling rubble which is likely when the writers intended for her to change her opinion of him, but even that was following him trying to destroy the school and the falling rubble was directly his own doing.
  • Strawman Has a Point: Magneto as always. He was presented as an extremist for believing that humanity and mutants couldn't co-exist and his plans to build an army of enhanced mutants to defend mutant kind were presented as villainous...but then when mutants are revealed to the world, they're met with hate, and until the X-Men proved that they could use their powers to protect normal people, the world was readying up to round them up and imprison them. Exactly what Magneto believed would happen. Though Magneto did reveal mutants publicly in the most shocking manner he could, seemingly to encourage this reaction from humans, but this was while they were battling the sentinel, a machine created by one of the few humans who knew they existed, showing that this view was always bound to exist even without Magneto's interference.
  • They Wasted a Perfectly Good Plot:
    • At the end of "X-Treme Measures", the creator of the drink promises Professor X to stop selling the drinks. But when Prof. X leaves, the creator gets out his phone and calls someone to tell them about it, with obvious malicious intent toward mutants. But it never goes anywhere and we never hear about it again. This, along with a few lose plot threads found in the fourth season, could probably be attributed to Marvel deciding to axe the series.
    • In the first season, it emerges that Magneto experimented on Kurt when he was a baby, resulting in Kurt's demonic appearance, and he is adamant that Mystique not tell Kurt anything about his past. What precisely was Magneto doing to Kurt, and why does he not want him to know about it? Your guess is as good as ours; it's never mentioned again.
    • Several plots and ideas were left hanging, including-but-not-limited-to Jean becoming the Phoenix and the debut of Mister Sinister, or the David/Legion plot, Gambit and Colossus potentially joining the X-Men, etc. The last season was only 9 episodes long, meaning that many of the plans they had couldn't come to fruition.
    • Several minor characters had hints of complex backstory elements, such as Ray's history with the Morlocks, or the tease that Colossus was Forced into Evil by Magneto, but ultimately none of this is explored. Piotr also had a Ship Tease with Kitty that never went anywhere.
  • Toy Ship: Multiple gets shipped a lot, despite being younger than everyone.
  • Ugly Cute: Nightcrawler and Toad. Nightcrawler even has some of this in-universe - judging by Amanda's reaction when she sees his true form.
  • Unintentionally Unsympathetic: Lance's romantic subplot with Kitty starts with him saving her life — from an accident that he caused. He had also previously attempted to attack Kitty, and due to the nature of his powers, he tends to cause a lot of collateral damage (sometimes near schools populated by children who are never confirmed to have gotten out alive). To some people, all this makes it kind of hard to believe that Kitty would want him for a boyfriend. This also puts him in the somewhat unusual situation of being a common victim of both Ron the Death Eater AND Draco in Leather Pants.
    • A weird inversion actually happens because of this. The time Avalanche did attempt a Heel–Face Turn, Scott doesn't buy it and proceeds to mistrust him. This is made out to be wrong of Scott, except, he is completely justified in mistrusting him: Lance was actually his biggest rival and had pulled crap on him and others before. While we (as the audience) knew that Lance was trying to do good things for Kitty's sake, Scott simply lacked such knowledge since Lance had given him reason to be antagonistic, and thus it's understandable to have him not trust Lance off the bat, and it would've been Out of Character otherwise.
      • The fact that Lance doesn't try very hard to convince Scott otherwise doesn't help him either. And the fact that Lance rejects Scott's heartfelt apology (after Scott found out that he had been wrong about Lance) and goes back to the Brotherhood really doesn't help.
  • What an Idiot!:
    • Not a life-threatening case, but a big one nonetheless. Spyke honestly did a research report on Star Wars when the subject was "The Star Wars". To an outsider, that's understandable... except in high school you only get an assignment after at least five weeks on a subject!
    • Another Spyke one: he uses his camera to record Wolverine's training session... while SKATING TOWARDS HIM! Also, his recording any mutant in general, especially since in the previous episode, they mention keeping mutant activites a secret.
    • One of the worst cases in show, however, is Mystique. Even though she's typically very competent, when she lets The Juggernaut out of prison and expects to able to just order him around and just plain insults when he doesn't act obedient, even though he has no reason to listen her. This would have ended in her death if the X-Men and the Brotherhood didn't come rescue her and Xavier.
      • Worse yet is during her fight with Storm in "The Cauldron, Part 1". Mystique apparently decides that recklessly kickboxing, drop-kicking, and outright throwing herself at the powerful weather-witch that can conjure up thunderstorms on a whim is better than using her shapeshifting and stealth to outwit Storm or morph into an animal/person that would pose a more significant physical threat.

        Even when Storm conjures up a cloud of Ominous Fog to obscure her vision, Mystique doesn't shapeshift into a bird and fly away, run out of the mist, or try anticipating a sneak attack from someone she could clearly hear shouting at her, instead standing perfectly still in the middle of the fog and gaping like a scared little girl as she sees Storm running at her from ten feet away with a very visible closed fist.

        And she achieves nothing from this brilliant strategy except for being electrocuted by high-voltage lightning bolts, knocked down a flight of stairs, blown across a room by a powerful wind, and blinded by thick fog, all before finally being punched out by a very angry black woman.
    • Lance often uses his powers inside. His power is generating vibrations to induce seismic activity (IE, make building-destroying earthquakes). His power has, on multiple occasions, resulted in buildings collapsing. He still uses his full power when inside, and more-often-than-not has to avoid the damage he causes himself.
  • The Woobie:
    • X-23 in her first appearance, especially when she breaks down in Logan's arms.
    • Kurt and Rogue also have shades of Woobiness at times, as does Wanda.
    • David/Legion, who was first told by his mother that his father Xavier abandoned him, then he moved to a new place where he had no friends, and then was slowly taken over by an alternate personality. An alternate personality that kidnapped and held him hostage in a castle. Then he gets permanently taken over when his dad tries to save him. Poor kid. Because the series was cancelled after Season 4, this becomes a case of The Bad Guy Wins, at least as it stands - there are hints he could've been still saved had the show continued...
    • It's X-Men, its one of the staples of the franchise is that (almost) every named character is a woobie in need of hugs. Scott has dead parents and uncontrollable powers, Jean's powers were shown to be extremely dangerous and hard to control despite how much she worked to appear to have them under control, Rogue had uncontrolable powers that she has no way of practising to use safely like others, Kurt had the whole 'my momma's evil' thing as well as his appearance making him quite isolated, Kitty was bullied for being too smart, Logan had no memory and was the victim to experimentation that he still has PTSD over... And that's just the important characters.

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