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, 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)? And if Jean really was just a Manipulative Bitch stringing Cyclops along for kicks... was Cyclops ever truly in love with Jean, or did Jean use her telepathy to make Cyclops fall in love with her and keep him in love with her long after they should have gone their separate ways in life?
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?
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.
Broken Aesop: Cyclops supposedly has to learn to let go of his grief & resentment at losing/being rejected by his Designated Love Interest (Jean Grey) and surrogate father figure (Professor Xavier)... only to learn that it was okay to hold on to the thin hope that Jean would be restored to him.
Despite the show being a Base Breaker, the voices for the characters here are often considered to be the definitive ones, especially in the case of Steve Blum as Wolverine.
Some fans still prefer the 90s voice actors, especially Cal Dodd as Wolverine.
Complete Monster: The Shadow King 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?
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.
Magneto arranging for the Sentinels to slaughter thousands of mutants on Genosha before intervening, then taking control of them for use as a vanguard in a genocidal war on baseline humans. Even in-universe, Lorna/Polaris and Wanda/Scarlet Witch disown and banish him from Genosha for his crimes.
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.
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 Nolan North going very over the top with it - though given the overall characterization of Cyclops he probably had no other option.
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.
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.
Cyclops's entire characterization and subplot is one big case study of unfortunate implications - his flashbacks portray him as clumsy and stupid instead of the competent, hard working student from the comics 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.
Hell, when you think about it there really was no good reason for Cyclops to even be featured on this series other than someone upstairs must have thought "Well people are used to him being there so let's just throw him in anyway." even if the way they did it made no damn sense and added nothing to either his character or the series as a whole. If Cyclops had been kept out of the series altogether it really wouldn't have impacted the story that much.
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.
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 them having a jet, while Mystique doesn't seem to have had any escape vehicle nearby.
Talking about the X-men's front door. After an exausting series of teleportations, Nightcrawler collapses infront of the school's front door where he is quickly abducted again. Apperently the X-men are completely incapable of watching their front door and actualy noticing their enemies being directly infront 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 retilates by throwing a 10 feet long piece of metal at her, while she keeps staring in suprise at it.
Talking about her. In her first appearance Marrow 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.
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 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.