Most people see X as either a strong but doubtful hunter who truly wants peace, or a spineless wimp who relies on Zero to save his ass at the slightest hint of danger.
Sourcebook info states that Dr. Light created a "suffering circuit" to enable X to examine moral matters more deeply. Does this mean X is putting himself through all this because he truly wants to make the world a better place for human and reploid alike, or did the 30 year testing phase in his capsule enslave him to Dr. Light's ideals? (At least the OVA clears this by showing that, while he hesitates sometimes, he fights Mavericks out of his own choice.)
Colonel himself can be subjected to quite a bit of this. In X's story, his decision seems to be made out of nothing but foolish pride. In Zero's, however, he's clearly shocked and outraged that the government would suspect him of being Maverick, and later in the story, honestly seems to believe that war is their only option, sometimes to a delusional extent. Given his backstory, it's certainly possible being faced with the threat of having his life's purpose taken from him caused him to snap.
Iris, Zero's romantic interest, varies from a saint, a seemingly sweet person who is secretly crazy, and truly sweet yet naive girl who just wants everyone to get along.
Thanks to the first game's remake, is Sigma just a Maverick infected by Wily who wants to dominate the world, or is he just staging a rebellion to test X's abilities in the interest of the good of the Reploids?
The entire "Maverick" thing. Canonically it's caused by viruses, but especially in the first and fourth games, there's very little to suggest that it was anything other than what it looked like on the surface: a rebellion. If that's what it was, were they necessarily bad? This is compounded severalfold by the fact that in the Zero series (same universe, just a hundred years or so later), the Irregulars are a genuine robot rebellion (and the good guys) against a tyrannical society which seems to hate all reploids, and the leader of their enemies is a copy of X.
Fanon popularly puts up a dividing line between "infected" Mavericks and just regular reploids who are criminals. What becomes of the latter falls into this as well — are they shot on sight in a display of Fantastic Racism?
Furthermore, there is a big case of What Could Have Been due to the extra characterization in Maverick Hunter X. Chill Penguin states that he follows Sigma effectively because of a bribe. Storm Eagle actually challenged Sigma and lost, so he's working with Sigma against his will. If the remakes continued, the "Regular vs Infected Maverick" angle may have been explored in canon.
The Rebellion / Liberion Army of Command Mission: Initially they seem to be a bunch of greedy, power-hungry sociopaths who cruelly oppress and subjugate everyone in Giga City — until you find that a few of their members (namely the Cadre) are surprisingly fair and honorable people, and the fact that they're the project of unethical experiments as well as being manipulated by The Man Behind the Man. Even Ferham, the seemingly sadomasochistic Baroness, has a genuinely tender moment with a fellow comrade. Their leader might even have a point that using force really might be the only way for a group of reploids to be heard. Despite all the horrible things they've done in the game, they're a hard lot to figure out, which is even reflected in the game when they're posthumously deferred Maverick status.
Despite what many of the Reploids they encounter say, neither X, Zero, or even Axl are ever shown to adopt a "shoot first" approach. More often than not, they ask them to surrender peacefully, are refused, and thus are forced to kill the Reploid in self-defense. However...some lines from Zero among others imply the Maverick Hunters prefer their officers to eliminate their target without wasting time. Is this policy because innocent humans and Reploids are in danger at the time and take precedence over violent Mavericks? Because each and every Maverick the Hunters have encountered have refused to surrender anyway? Because of the danger a possibly viral Maverick or one feigning surrender presents? Or is their a racist anti-Reploid agenda behind it?
The humans themselves, particularly the government. Not helped by the fact that humans rarely get their own views, or even appearance, shown in game (the only human we see, Dr. Cain, even disappears after X4). Are they well-meaning, seeing the Reploids as equals and valuing the hard work they do, or do they refuse to see the distinction between them and the Mechaniloids (which are literal machines) and are only happy as long as the Reploids do what they want, as Sigma believed? As for the trust issues, are they simply being Properly Paranoid about them given their capabilities, or are they fanatical bigots like Weil, who felt the entire race "got off too easy" because of what the Mavericks did, and willing to take extremes to control them?
Did Sigma go maverick because of the virus or did he become maverick of his own free will? The main continuity confirms the former, while the Maverick Hunter remake implies the latter. There's honestly probably room for both origin stories. Sigma was designed to be the leader of the Maverick Hunters, where we see him in The Day of Σ OVA. Dr. Cain most likely instilled him with an inherent admiration for the reploids he was meant to command. Perhaps the virus corrupted that admiration, turning Sigma in to an Anti-humanEvilutionary Biologist. X8 implies that it was indeed both. When confronted by Zero, Sigma explains that the virus set him on his current path; but when confronted by X, he reveals that it was X's dedication to justice that first got him thinking about how imperfect the world was. In other words, X inspired Sigma to think about the world's ills while the virus prompted him to act on those thoughts.
In X8, it is revealed that the New Generation reploids (and by extension, Axl himself) were built via the manipulations of Sigma, who considers them his children. This bothers Axl roughly a thousand times less than Zero's similar origin eats at him; in fact, he's the only one of the three not driven into a Heroic BSoD by this "Break Them by Talking" done soon after. It helps that:
Sigma and Lumine don't press the point (when Axl outright asks Lumine whether Sigma's influence will affect his sanity, Lumine dismisses him), unlike what Sigma does with Zero.
Zero was having nightmare visions of a certain crazy, eyebrow-waggling old scientist even before Sigma started playing with his head.
Axl has a lack of angst over being forced to kill his adopted father in X7. In his defense, Axl didn't really deal the killing blow. He just beat the guy in a fight. It was Red's decision to set the place to blow if he lost and to go down with it.
Dr. Doppler in X3. His attack pattern is almost insultingly easy, though his ability to absorb your attacks can make the fight seem harder than it is.
Iris in X4. Compared to Double in X's route, Iris isn't terribly difficult. Justified as Iris was never meant to be a fighter and the project that spawned her and Colonel, spawned the two for a reason. note They were originally one and the same reploid meant to replicate the paradox X had with technical pacifism, but Iris' innocence and pacifism doesn't go well with Colonel's spirit of combat and honorable nature, so they were Split at Birth.
X in X5. You realize how inconvenient charge attacks are when they telegraph every move X makes as a boss. You'll also realize why it's important to move while charging.
Zero in X5. Also like X, the battle isn't very spectacular because Zero's AI makes him spam his easily avoided (with some practice anyways, but you're certain to get some) Giga Attack over and over again. This results in a decidedly unspectacular battle.
Sigma in his X6 form, especially since he's fought after Gate (and his goddamnedlaboratory). Subverted for his second form, however.
Just like Wily, Sigma's constant defeats makes him less and less of an imposing villain with every game, to the point that in X6 he's reduced to a mentally unstable zombie who can barely form a coherent sentence. Somewhat reversed for X5, however, where the Eurasia Colony Drop he instigates has lasting consequences in the Mega Man Zero series.
While Vile remains a formidable boss in X3 and X8, he never regains his dreaded Hero Killer status from the first game, where he curb-stomps X and Zero and requires a Heroic Sacrifice from the latter for the former to even stand a fighting chance.
Many fans believe that X series should've been put to rest at X5, as many key plot points (such as X and Zero's destiny to defeat each other despite being best friends) were resolved there, and the plot picks up in the fitst Zero game. Inafune even indeed stated that the game has the "finality" feel to it. Others would be fine with seeing more X games to stick with the characters and expand on the plot points introduced in the later games. Of course, by this account, X5 is still the end of the series, as each post-X5 game has a time period during the three years the epilogue states, while X6 took place after Sigma's defeat in a few weeks of X5. As an additional note, Zero's ending in X6 is supposed to take place after the end of the series, allowing sequels to be made. Of course, the debate won't stop even with that.
Whenever X3 is brought up, expect to see much discussion on which has the better soundtrack, the SNES version or the PSX/Saturn version.
Dr. Albert W. Wily, thought long dead, is, in truth, the Greater-Scope Villain of the entire series. With nothing resembling his more honorable traits from the Classic series, Dr. Wily created Zero as a means to finally create a robot strong enough to destroy Mega Man, and engineered the creation of the Maverick Virus, turning Reploids who were infected to violence and murder. Wily integrated himself into the virus itself and fostered countless amounts of death and destruction, most notably causing the fall of the once-noble Reploid Sigma to ambitious evil with thousands killed in his mission, and even nudging Sigma into trying to cause the fall of the colony of Eurasia to spread the virus further, which would consequentially kill off almost all mankind.
Continuity Lockout: Zero's ending in X6 is said to take place after the very end of the X series. However, Zero's presence in X7 and X8 is highly confusing to most fans because the status of Zero's X6 ending is only revealed All There in the Manual in the Mega Man Zero Official Complete Works.
Die for Our Ship: Some fans aren't fond of Iris for being a brief love interest for Zero, getting in the way of the popular X/Zero pairing. Since Iris dies in her debut game, it's mostly a moot point.
Dork Age: X6 and X7 are generally considered to be a slump for the X series; the former for its rushed development and cobbled-together level design resulting from it, and the latter for its clunky gameplay, bland level design, and misguided attempt at bringing the franchise to 3D. Many will say X8 was an admirable attempt to get it out of the slump and an improvement over the former two games, but sadly, the damage had been done by then, and a new game in the series has yet to surface.
Draco in Leather Pants: Fangirls like to think that Vile is secretly sexy under his helmet and try to slash him with X (despite trying to kill him multiple times), and that Dynamo is a lovable goof who joins the Hunters and is paired with Alia (despite nearly destroying the world with a Colony Drop). Lumine is also starting to get this treatment.
The Green Biker Dude from Mega Man X2. They're just a generic reploid who appears in the background of the intro stage and gets shot down in an instant, but gets much appreciation for their sacrifice. Being able to do some wheelies with their Ride Chaser helps.
iX, a manga-only character, is especially popular among sprite fan artists.
Iris only appeared in one game in the main series, but fans tend to be happy whenever she reappears, such as in Mega Man X-Treme 2 and as a NPC in Project X-Zone.
Marino is only present in the Command Mission spinoff, but is well-liked for being a playable female reploid. Cinnamon from the same game applies to, to the point where she was one of the first revealed playable characters for Mega Man Online.
Body Surf: See the theory about the X-Hunters below. Also, Isoc from X6.
Alternately, he's just using the Time Skimmer he used to obtain Quint.
Speculation on whether or not Serges is Dr. Wily, because of his physical resemblance and strange interest towards Zero. An even more outlandish theory is that Wily somehow "lives on" in all three X-Hunters.
To elaborate, Serges was able to repair and upgrade Zero (or possibly made his new body entirely from scratch), despite Zero being notoriously difficult to analyse and repair, due to his Black Box status. Arguably, the only one who could show such an understanding would be Wily himself. Also, in the Japanese script, he expresses regret over being defeated by "Light's robotic memento". Maybe he just knows his history?
Made worse by the fact that the manga adaptation leaps to the conclusion that Serges is Dr. Wily.
Due to Axl's ending, many fans suspect that Lumine has somehow transferred his consciousness into Axl after his defeat.
Estrogen Brigade: Mega Man X has a very strong female following, especially in comparison with other entries in the series. For how action-packed it is, the strong focus in X/Zero relationship, how much the games are dripping in Ho Yay between the two of them and the drama help make the series appealing to both sexes. It also helps that Zero is handsome and mysterious with a tragic past.
It has been a long debate whether the series after X5 (where Zero really died) was canon. However, an official artbook released for the Mega Man Zero series subtly hints at their canonicity. Doesn't stop some fans from disputing the issue, though.
Some fans completely disregard the Guns N' Roses names for the X5 Mavericks, and refer to them by their Japanese names instead. The version of X5 found in the second X Legacy Collection switching to names closer to the Japanese originals only helped this stance.
The first stage is called "Noah's Park", a space elevator is named "The Jakob Project" after Jacob's Ladder, and the final boss appears as a fallen angel whose ultimate attack is called "Paradise Lost".
Sigma's true form looks demonic, is called Belial Sigma, and is weak to light-based weapons. Fans have also likened Lumine's name to that of Lucifer, the "light-bearer" and fallen angel who would eventually become Satan, due to the aforementioned angel motifs. Similarly, the Mavericks' plot to migrate to the Moon and escape a war-torn (and thus useless) Earth is seen as an allusion to the story of Noah and the Flood.
First Installment Wins: The first Mega Man X game is often considered the best, evolving the classic Mega Man series to faster, more complex platforming, along with new gameplay features and a more mature storyline, and no subsequent game has gotten the same praise. X4 is the only one that comes close, with some fans regarding them as even even better than X1. Many other games in the series are still popular, but they tend to be contested in a few areas that leave them out of the same league as those two games.
One of the criticisms of X7 is that X himself got shafted to being unlockable, becoming a bit player in one of his own games. This had always been a bit of a problem, specifically because Keiji Inafune apparently regretted his decision to withdraw Zero's design as the lead and deliberately was giving the X the short end of the stick to make people like Zero more. It started in X2 which gave hints of Zero's origins and a sidequest about bringing him back to life, but that was okay since it gave the series another cast member. But when the Playstation era started, X was just along for the ride while Zero got all the big character interactions and backstory in X4 and was pretty much the sole reason for X5. While X6 was a little better, Zero still hung over the plot and two of the endings were sequel hooks for the Zero series. Hence, X being dropped as the lead for the next game was the obvious endpoint. Command Mission and X8 addressed this with X getting equal or more screentime compared to his partners while Zero mostly did his own thing in the Zero series.
The criticisms of X being a whiny protagonist can be traced all the way back to the first game, with X already angsting about having to kill Mavericks and the heavy losses that came with the war against Sigma. The main difference was the limitations of the hardware at the time made longer cutscenes more difficult to put in, thus keeping it from being really at the forefront, and he was still willing to hunt Mavericks for the sake of protecting people. As the games went on and the hardware improved to allow for more fleshed out cutscenes, in combination with Zero being a Spotlight-Stealing Squad in the later games, X's pacifistic side became more and more pronounced to give him some relevant character arc, reaching its zenith with X7, where X's characterization of trying to find a peaceful way to deal with Mavericks became flat-out unlikeable and illogical for many.
Dashing at an enemy while firing a normal shot dealt double damage in X and X2, which was fixed in the third game and beyond.
In X8, Zero (and Layer) can fly!Note Contrary to popular belief, this isn't limited to the PC version of the game, as the PS2 version uses both the D-Pad and the left stick for movement, so the glitch can be performed using both. The X Legacy Collection 2 version of X8 however fixed this bug.
In X4, standing on Colonel's saber swing area when he fires his Sword Beams doesn't do any damage.
Vile in Maverick Hunter X can use his shoulder or leg weapons to stop his descent, allowing him to move horizontally through the air. Use a weapon with low enough energy requirements and you can practically levitate into places early that would normally require a late game weapon upgrade for. This might be a case of Throw It In!, as stopping Vile's descent using the weapon drops is the only way to avoid getting hit by X and Zero during a certain attack phase.
Growing the Beard: Many believe that the X series did so with the jump to the PlayStation, which allowed both the gameplay and story to reach new heights that they never could have within the SNES' limitations.
At least in story order — while X taking a beam saber through the chest in The Day Of Sigma cues a Moment of Awesome, it's also reminiscent of something more permanent that happened to him later on, especially considering the parallels drawn by one character between Sigma and Elpizo.
In the same OVA, Sigma launches a missile strike against Abel City (although with the intention of giving Reploids a future). In Zero 3, the Neo Arcadian Government (specifically Copy X and Dr. Weil) launched a missile strike against Area Z-3038, a human population, of which the missile contained Omega, so they could acquire the Dark Elf, an action that was implied to have resulted in severe casualties in the city.
Also, in X4, Sigma tells General that humanity, and by extension the Maverick Hunters, are perfectly willing to destroy anything that doesn't obey humanity absolutely. The Zero series shows just how correct Sigma turned out to be, with the main bad guy in Zero 3 even stating that humanity enjoys controlling everything, considering it to be the ultimate joy. However, he, Weil, is the only human shown to feel that way, and ironically, is almost exactly like Sigma in terms of his megalomania, self-serving morality, and appetite for death and destruction, the only real difference being Weil's bigoted against Reploidkind whereas Sigma looked down on humanity.
The ending of X2 has Zero easily destroy a weaker clone of himself. Come the Mega Man Zero series, and Zero ends up being the clone himself, with his original body being substantially more resilient.
The X3 finale. X scrambles desperately away from Sigma to avoid possession and freaks out at a dead end, then Dr. Doppler or Zero shows up and gives his life (minus the sacrifice in Zero's case) so that Sigma will not infect X with The Virus and take over everything with all the wonderful armors and weapons and whatnot. It turns out, Sigma can't actually do any of this; the whole thing was pointless. However, X5 establishes that critical infection causes harm to X, so Sigma still could've killed him by trying to infect him.
Martei, a mermaid-based Reploid who becomes X's Love Interest in the manga, was introduced before the release of Mega Man 9, which included mermaid Robot Master Splash Woman. The original Mega Man is sometimes shipped with her.
Egregion, the enormous dragon intro stage boss in X4, who was originally named Eregion. Apparently named from one of J.R.R. Tolkien's works, yet it also brings to mind another piece of literature.
Up until the release of X4 and thus his decidedly male voice, due to his long blond hair and "booblights", Zero was often mistaken for a woman. Come the ZX series and Zero is now a Biometal, which merges with the player character, one option of which is a girl.
This is a series with characters named Sigma and Zero. Many years later, the Zero Escape series would also feature major characters with these names.
Zero was supposed to be the protagonist of the series, until this idea was nixed because the devs figured that making a protagonist too dissimilar from Mega Man would alienate fans. Almost a decade later, when Zero became a major Breakout Character more popular than even X himself, it now made sense to give him his own series.
It Was His Sled: Almost anyone remotely familiar with Mega Man knows that Zero was created by Dr. Wily, a twist not revealed until X5.
The ever popular "WHAT AM I FIGHTING FOOOOOOOOR????!!" from X4, no less due to the really poor delivery of Zero's (and Iris') voice actor. It is, otherwise, a suitably tearjerking scene, especially with the original Japanese voice acting.
"Take a wild guess!" note When X demands Split Mushroom to reveal who his boss is, Mushroom responds with this. Cue his Life Meter appearing with a Sigma logo underneath.
On this site, there have been times that either of the series' two incarnations of Zero has been compared to this Zero.
Alia's "upgrade" in X8.
The Ze-ERO series, a series of MADs (a rough equivalent of YouTube Poop) that mainly involves characters from this series, on Nico Nico Douga (and some of it have been exported to YouTube as well). Warning: NSFW.
"I hid myself while I tried to repair myself." Said scene in X6 (where Zero reunites with X) is especially popular in Japan, with many fanarts parodying it. To be specific, the Japanese thinks their facial expression look more appropriate for Zero trying to make X a boxed lunch and X being happy to be given it. The meme's called "Obentou" (Boxed Lunch), from Zero's quote in the meme: "I woke up early and made this boxed lunch for you". The parody is done between two other characters in other fictions, especially with the "Zero" figure being a character thought to be dead (like Zero was in X6).
"LISTEN TO ME!" - Palette's nagging quote if you set her as your operator in X8, particularly if she finds a secret in a level.
HIS NAME IS DUFF MCWHALEN!!Explanation After the removal of Guns N' Roses references in Megaman X 5 for Legacy Collection, Duff McWhalen becomes a meme icon to protest for the name removal, because his original name, GNR reference aside, is just so stupid it's endearing. The video was the most prominent meme evolution, where the narration launches a tirade about his flaws (weak weapon, level being That One Level, song is a remix of Bubble Crab stage, and his name), but delivered in such hilarious frustration that the phrase becomes the rallying cry mentioned almost everywhere when Duff is mentioned and made people insist to call him Duff McWhalen instead of the more default Tidal Whale.
Moe: RiCO from X Dive immediately hit super-duper moe status thanks to her voice and perky nature.
He really starts crossing it in X3, X4, and X5. In X3, he corrupted Doppler and halted an effort that was leading to end to the Maverick Wars. In X4, he manipulates the Repliforce into fighting the Maverick Hunters, causing the events of the whole game, and in the end tries to decimate the Earth with the Repliforce's Kill Sat. His biggest is in X5, when he spreads the Maverick Virus across the planet and plans a Colony Drop with the infected Eurasia just to get Zero to go Maverick, and dialogue with X shows him saying that he figured the Maverick Hunters would keep the planet from being completely destroyed, but he clearly doesn't care about the damage caused even if it wasn't world ending.
The Repliforce War is implied to have been this for the unseen previous commander of the Maverick Hunters as said commander resigned in disgrace following the end of the conflict, resulting in Signas becoming the new commander.
More Popular Spin-Off: At the beginning, the Mega Man X series was seen as more appealing than the Classic series, but this is not as evident now due to the divisive nature of the later games.
The sound of Zero's buster charging before he saves X at the start of X1.
The SNES sound of X's buster charging is quite wonderful to hear.
In the SNES games, that extra-loud hit sound whenever you land the final shot on a Maverick.
Motive Decay: Invoked with the "Maverick" label, which over the course of the X and Zero series goes from "Reploids infected with the Sigma virus" to "Not infected but still heavily armed and posing a threat" to "Political dissidents the powers-that-be want disposed of."
In Maverick Hunter X, Vile tends to act like an angry child half the time, leading to situations where he erupts into a tantrum because Armored Armadillo, who he'd previously been mocking, said he pitied him, and one where a civil conversation with Storm Eagle turns into a death match because Vile apparently doesn't like his face.
In X4, the poor voice acting ruins what is supposed to be a legitimately affecting scene between Zero and Iris. Though this one crosses with Narm Charm because of how poorly delivered the entire death scene is. It strengthened Zero as a character, because people will NOT forget it.
Narm Charm: Silly as Vile's tantrum's in Maverick Hunter X may be, the fact that he'd blow away potential comrades over a comment that was made in response to his own insults, or because he didn't like a guy's face is terrifying, and those cases are the few where he actually has any reason at all!
Fans like to make fun of how frequently Zero dies, to the point where it's his primary character trait in some portrayals. While the number of Heroic Sacrifices does get a bit ridiculous in the two following series, X-era Zero — who is shown by fans as the poster boy of dying — canonically only dies twice in the eight main series X games.
There's quite the contingent of fans who mistake X for a whiny, hypocritical wannabe-pacifist because of his portrayal in X7, ignoring all of his previous characterization that establishes him as nothing of the sort.
Sigma coming back from the dead and/or being revealed as the games real villain in almost every game in the seriesnote Though in X5, this doesn't happen as Sigma is acting out a plan made with a partner who's implied to be Dr. Wily, and in X6 and X8 he technically wasn't the main villain, but was simply resurrected as a convenience by Gate and Lumine respectively, and he's completely absent from Command Mission. is another infamous cliche that fans will never let the series live down.
So the series finally allowed Zero to be fully playable? Iris dies. In fact, she was probably introduced into the story just to invoke the trope to Zero.
Zero ends up being a major player punch when he kamikazes Vile in the first X game. And it also seems that X himself channels the player punch by breaking out of an electrocage, having his health refill and his weapons restored. Then it comes up again after defeating Vile with the conversation, and gift, that will gives X if he didn't get the buster upgrade. The Maverick Hunter X remake makes the scene hit even harder.
The Mega Man X Collection adds a save feature to and removes slowdown from the cartridge-based games, and significantly reduces loading times for the disc-based games. That said, this collection is prone to some annoying input delay, although this can largely be adjusted to by the player.
The Mega Man X Legacy Collections take this a step further, adding a slew of new features, including a newcomer friendly "Rookie Hunter Mode" that reduces much of the damage from everything and the "X Challenge" mode that lets the player fight two bosses (often from different games) at once.
Popular with Furries: As expected in a series where you battle robot beastmen. Neon Tiger from X3 is particularly popular, even having his own Wikifur page.
The iOS port of the first game. Not only does it load less smoothly than the SNES version (despite the system being more powerful), it contains poorly redrawn graphics, generic text, and a lot of the artwork cribbed from the PSP remake of the game, which they could have released a modified port of instead. But here's the kicker: you can buy all the weapons and health boosts with real money, without acquiring them the proper way, from the very beginning of the game. This was considered a bad look during a time period where Capcom wasn't treating the Mega Man series well.
While "disaster" might be too strong a term, the Legacy Collection versions of the games suffer from very noticeable input delay (with X1 having it the worst), and the Steam version launched with a bug that could to lead to significant framerate drops and slowdown (though this could be fixed with a simple tweak). Mind you, the games are still perfectly playable this way (this is still largely a Polished Port), but compared to the original versions, the controls simply aren't as responsive or tight.
Relationship Writing Fumble: X and Zero are just friends in canon, but they often act like a bit more. No wonder fans use them as the biggest source of Ho Yay in the series.
Alia as well in X8, due to having a more tolerable voice and being a hidden playable character. X6 did the first step by making most of her dialogs optional and more pertinent, and giving her some backstory.
Sigma in X4, X5, and X8, for toying with the Repliforce and Maverick Hunters like fools, attempting to blow up the Earth with an infected Eurasia Colony, and playing an active role involving the Jakob Project.
YouTube Let's Player HideofBeast takes this to downright masochistic levels, having done a minimalist, no damage speed run of X4 through X6on Extreme Mode. This is especially painful when you take into account the horrid level design of X6 and how much of a pain in the ass it is just to beat it normally.
Playing as Zero from X4 onwards, especially Black Armor Zero. He's a lot more mobile than X and his saber has better DPS, but he takes more damage from attacks than X does and he has very few ways to attack from a distance, leaving him much harder overall to master.
Rescuing hostages, especially in Mega Man X6 and X7. Not only do they possess important parts that are Permanently Missable if you screw up, but rescuing them can be a Luck-Based Mission at times as well.
The aptly-named Nightmare System in X6. Whenever you complete a level, two other stages become affected by the Nightmare Phenomena, which amounts to making those stages much worse to put it lightly. For starters, giant metal blocks that crush you against floors or ceilings, pitch-blackness over the stage, or even fireballs coming at you.
Sequelitis: After the original game (which, as mentioned above, is often regarded as the best in the series), there seems to be a "rule of two" as to the quality of sequels. X2 and X3 are regarded as decent, but not offering a whole lot over the first game other than being able to play as Zero in the latter sequel (and even then in a very limited way). X4 is seen as a major step-up in quality and the best game after the original, and X5 is also generally considered to be pretty good, although it has received criticism because of some mechanics and the level design. X6 is regarded as an overly difficult Mission-Pack Sequel with poor level design and a ton of annoying game mechanics, while X7 is not only considered to be easily the worst game in this series, but arguably the worst Mega Man game of all time. Command Mission and X8, while not exactly masterpieces, are if nothing else regarded as way better than the two previous games, and not too bad by their own standards.
Strangled by the Red String: Iris appears in one game (assuming you don't count the Xtreme series), only for said game to kill her off (there was the prequel, but there's not much in that game regarding their relationship). The end result is that her relationship with Zero feels rushed.
In X5, Awakened Zero's Genmurei, a gigantic Sword Beam attack that is a One-Hit Kill and only used if the battle lasted long enough.
X8's Bamboo Pandamonium's Desperation Attack, a lunging attack that takes off half the screen, comes off without warning and does obscene damage.
Lumine's first form uses the desperation attacks of the eight Reploid bosses, including the one mentioned above. However, there are two attacks that he modified; Avalanche Yeti's attack, which causes gigantic snowflakes that freeze you on contact to rain down, lasts a lot longer, and Lumine can still blast you with other attacks while it's in effect. And then Burn Rooster's attack, which engulfs the walls in flames, never wears off. After it hits the field, you can no longer wall-jump. In his second form, when his health dips low, he uses an attack that opens up a rift in space. If you don't kill him within 30 seconds, you die, game over, no matter how many continues you have.
Any mission involving the use of the Ride Chasers. Ironically, X6 doesn't have any of these levels, though most of the game's stages are Scrappy Levels enough. X8 made up for it with two Ride Chaser stages, though.
The only level in X8 that isn't a total pain in the ass is Bamboo Pandamonium's stage, which becomes pretty hard if you're going for 100% Completion.
Later versions of X3, such as in the X Collection, used the PS 1/PC version of X3, replacing the synthesized SNES music with arranged versions, and the classic X sound effects were completely replaced. Not everyone was happy about that. Thankfully, the Mega Man X Legacy Collection included the original SNES version of X3 instead of the enhanced version.
There's a short prophecy that was introduced at the end of X3, stating that "To save mankind, X must destroy Zero". Two games later, the prophecy was fullfilled, but in a twisted way. The battle doesn't involve the fate of mankind directly (at least in the true/canon ending; the alternate path, however, shows another side), but instead it's simply about a question of trust between two friends.
The whole thing about Dr. Wily being alive somehow that started in X5. There, it was blatant, with his giant logo in the background, a Nostalgia Level and bosses, and Wily actually talking to Zero when he awakens his Super-Powered Evil Side. It was all but dropped later, with only a few subtle hints in X6, regarding Isoc, and from then on absolutely nothing. Rumor has it that Executive Meddling made them drop it because it was supposed to be resolved in the Zero series, though it never was.
Tough Act to Follow: Mega Man X1 left such a strong impressio that the rest of the series had a very difficult time matching it. The only game that fans consider to come close is Mega Man X4.
Toy Ship: Axl is often shipped with Pallette or Cinnamon, both considered young characters.
Uncanny Valley: Gamma Sigma in X5. Seeing its pre-rendered face in a game full of traditional sprites adds to its creepiness.
Unnecessary Makeover: Alia's redesign after Mega Man X8 has been rejected by many fans since they see it as an unnecessary attempt to make her a Ms. Fanservice despite already being attractive and a change that undermines her role as a scientist and a major Maverick Hunter.
Because of his long hair, sleek body and odd-looking lights on his chest, many people unfamiliar with the series think Zero is a girl at first.
Lumine. It's difficult to explain without looking at him◊. His womanly voice doesn't help.
Visual Effects of Awesome: X2 and X3 including the Cx4 chip that allowed for usage of wireframe graphics, like the Final Boss of X2. The developers made it a point to show it off in the games as much as they could find excuses to do so, and the times they use it are very memorable and stand out against the normal sprite-based enemies.
X and Zero (especially the latter) go through a lot of undeserved suffering in their fight to save the world from the Maverick Virus.
Some of the Mavericks that were infected or deemed Maverick, most notably those of the wrongly accused Repliforce in X4 (regardless of the irresponisibily of its leaders).
Iris in X4. All she wanted was peace between the two forces, yet this sweet innocent girl got thrown into two forces fighting for their beliefs and she's torn in which side to pick, leading to her brother Colonel getting killed by Zero, and her going past the Despair Event Horizon before too being killed by Zero.
Woolseyism: The name change for Bit and Byte in X3 changing them from an obscure mythological reference into something memorable, if not a bit goofy.