The game more or less spells it out that Ciel has feelings for Zero short of actually confirming it. Fans have then speculated that the final line of the series might have actually been an Anguished Declaration of Love.
Dr. Weil, even from the start, had pretty warped ideas of right and wrong, blaming the entire Reploid race for the crimes of the Mavericks and intending to make a way to control them all. It's entirely possible all the suffering and destruction around him at the time (Going through the main series alone; The Maverick Wars, the fall of Doppler Town, the Sky Lagoon Disaster, Repliforce's rebellion, a colony drop, the emergence of yet another strain of the Maverick Virus, the Red Alert rebellion, and a large-scale rebellion by the new generation reploids, all in his lifetime) left him severely unhinged.
Another point for Weil is that the Colony Drop he was planning might be the only means he thinks he has left to finally die, and his Villain Ball during the final act of the game is actually an act of goading Zero into finishing him off.
Despite all of the buildup to him in the first game, Copy X is a surprisingly easy final boss, especially compared to the bosses and Four Guardians you just fought again beforehand, mainly due to his predictable, easy to avoid attack patterns and lack of stamina. The second phase has a few cheap attacks at its disposal that'll kill Zero in a hurry if you let your guard down, but as a trade-off, you can defeat him with just a few fully charged Z-Saber strikes. It makes sense from a story standpoint, since it hammers home that he's an inferior copy of X.
Elpizo from the second game. If you can avoid his six-orbs energy absorption attack, you can pretty much dodge anything else he throws at you. His second form is arguably even easier, basically being a large floating target in the middle of a large empty walled room with easy-to-dodge attacks. Compare this with the spike-laden stage that you have to traverse to get to him, as well as the Boss Rush in between. A few blows from your charged Z-Saber will destroy his second form in a matter of seconds.
Omega's first 2 forms, thanks to the GBA limitations, are slower and more predictable than what is implied from the story.
Anubis Necromancess III's attacks are relatively easy to dodge, although both the Zombies and the scepter deal a lot of damage. The technique of the crushing structures is fairly easy to avoid.
Fairy Leviathan is arguably the easiest of the four Guardians normally. She makes up for it later, while Fefnir actually got somewhat weaker. Harpuia in the first game, however, stands out as being a total idiot who doesn't know what to do about being hit with ice attacks. He will always respond to one with the same attack where he sends three shockwaves, one low, one high, and another one low. This takes long enough that you can build up another charge, even without a fully leveled weapon (or in Hard Mode where the Shield Boomerang is the only thing you can charge) and weave through to clock him again. Rinse, repeat, and he's down with minimal effort.
Broken Base: Whether the original plan to have X himself be the villain of the first game rather than Copy X would have been a good idea or not. Some fans think it's a good thing it didn't happen and that it would have derailed his character, not to mention it would prevent the entire ZX series from being a thing. On the other hand, a lot of people feel that it was an instance of wasted potential and would have been much more interesting and emotionally resonant than what actually happened (especially considering that foreshadowing for it exists in the X games themselves).
Catharsis Factor: You get to cut enemies and bosses in half. Why stop at just shooting them dead?
Complete Monster: Dr. Weil, known in Japan as Dr. Vile, only appears in a few games, yet is notable for being one of the most evil beings in the entire franchise. Following the peaceful resolution of the Maverick Wars by the sentient superprogram, the Mother Elf, Weil decided that Reploids needed to pay for their crimes. To this end, Weil corrupted Mother Elf by turning her into the Dark Elf, and triggered the Elf Wars. Weil used the Dark Elf and her children, the Baby Elves, to control Reploids and force them to fight each other in massive battles, which resulted in the deaths of 90% of all Reploids and 60% of all humans. Defeated, exiled and transferred into a mechanical body for his crimes, Weil eventually returned one hundred years later, consumed with a thirst for vengeance directed at all life for the perceived crimes against him. Weaseling his way into becoming the supreme ruler of Neo Arcadia, Weil turns it into a dystopian hellhole. When he breaks his citizens to the point where they're desperate enough to risk escaping into the wastelands to form their own colony, Weil decides to obliterate their new home with a Kill Sat. When his Kill Sat is disabled, Weil attempts to drop it upon the colony, killing everyone in the region. Cruel, megalomaniacal and displaying an unprecedented level of sadism in the series, Weil reveled in the suffering of others and desired nothing less than to make human and reploid alike feel like their existences were living deaths.
Contested Sequel: The opinion on whether Zero 4 matches the quality of the previous two games varies. Some consider Zero Knuckle, the chip system and having only one Cyber-elf major innovations, while others don't think they quite match the part system and the Satellite-elves of Zero 3. However, almost everyone can agree that Zero 4 wraps up the overarching storyline of the saga in a very satisfying way.
Ending Aversion: Over a decade later, there are still some fans who take issue with Zero's death on the grounds that he should have at least been allowed to live long enough to see the better world his efforts created. Mega Man ZX having him reborn as Model Z gives him that chance, but some still aren't satisfied.
Enjoy the Story, Skip the Game: Some fans are taken aback by how Nintendo Hard it is, but these games generally are considered to have the best story in the Mega Man franchise. Luckily, the Zero/ZX Legacy Collection has the Casual Scenario mode which eliminates the difficulty altogether for those who just want to enjoy the story.
Despite only serving as a recurring antagonist for the first three games, Harpuia is beloved for being one of the most well developed characters in the franchise, as well as for being a Noble Demon that becomes increasingly more sympathetic as the series progresses.
Pretty much every Guardian has some degree of darkhorse status; they all have really fun fights, they're all interesting characters, and something unique to each one makes them stand out. Leviathan is one of very few Mega Man water bosses to combine high mobility with difficult attacks for a fun fight (as opposed to most water and ice aligned bosses, who are dull and slow), Phantom just in general oozes Rule of Cool (he rides a shuriken while throwing more shurikens at you), and Fefnir is Hot-Blooded in all the right ways. It's no wonder they functionally became 'playable' as Biometals in the sequel series. Plus, three of them (Harpuia, Leviathan, and Fefnir) pull off a pretty cool Heroic Sacrifice to help Zero beat Omega, and Phantom has a really fun Bonus Boss fight in 3.
Even Better Sequel: Zero 2 was already a Surprisingly Improved Sequel for Zero 1 but Zero 3 perfects the formula. It is widely considered the best in the series and one of the best Mega Man games ever made. Satellite-elves were considered the most obvious improvement, as you could mix and match between two of them at any point in the game without affecting the rank. This game also introduced additional head, armor and foot parts you could customize to your liking. Of all the new weapons, Recoil Rod was praised for being more or less a combination of the best parts of both Triple Rod and Chain Rod note The stage design, boss fights and finding secrets greatly encourages the use of Recoil Rod. The weapon skills were scrapped altogether, meaning you didn't have any need to grind anymore. The story was also considered the best with increasingly higher stakes and has a more interesting and menacing villain in Dr. Weil when compared to Copy X and Elpizo in the previous entries.
Evil Is Cool: Copy X's armor would spectacularly break any Mega Man X game, essentially being X5'sFalcon Armor with extra firepower and Charge Man's weapon thrown in for fun.
At the end of the first game, Cyber-Elf X starts projecting an image of himself in a blue robe when talking to Zero. A Cyber-Elfy halo appears above his head in this form.
Copy X. If his first form full of angelic wings isn't enough, in his One-Winged Angel form, he almost literally turned into a seraphic angel. Add to the fact that he's fighting Zero, a crimson-horned reploid.
Fanfic Fuel: The ending of the series. The fans don't seem to accept Zero's death, and as Dr. Weil cannot die, they "know" he's still out there. There's also the fact that there's around a century or two of Time Skip between this series and Mega Man ZX. The general agreement across different fan groups is that Zero perished in his Heroic Sacrifice but was successfully resurrected by Ciel in ZX as Model Z.
Goddamned Bats: The spiked wheel enemies. They are inordinately tough (two saber slashes when one will do in most anything else that moves), coming rolling from offscreen towards you (or occasionally from behind) with no warning, do a ridiculous amount of damage (more than virtually any other normal enemy), move just fast enough that it would take split-second reflexes to dodge them, spawn again if you move mere pixels backward from where they appeared, and are sometimes dropped in by lifter robots for added cheapness.
Volteel Biblio of the third game; a large portion of his fight is akin to a whack-a-mole, except that the holes are spread far apart. His head will appear in one hole while his tail will appear in another, shooting a slow homing ball of electricity.
Pegasolta Eclair of the fourth game has a clever but annoying tendency to fly up to avoid your attack. He can only be attacked if he's attacking, which you'll have a hard time with since spends most of his time far from the ground.
Mino Magnus is positively annoying: He's weak to ice attacks, but his hitbox is often obscured by his invulnerable shoulders. His magnetizing Grapple Move will cripple you and make you more vulnerable to his magnetic attacks, and his Detachment Combat attack needs quite the timing and fingerwork to avoid.
Good Bad Bugs: The Orbit Shield. Basically, there are two flavors. The first is where you throw the Shield Boomerang, then rush forward and start jumping over it so that you don't catch it and it goes in a circle indefinitely, and the other is the "automatic" version where you jump and throw it against something it'll bounce off of, allowing you to stand idle and let it do its thing (orbit around you, hence the name). While its utility is pretty limited, it makes for a fantastic method of leveling up the Shield Boomerang by making it so you don't have to charge it over and over, as you can do the automatic version in both Zero 1 and Zero 2 (In Z1 on the infinitely recovering tower enemies in the overworld version of the second stage, destroy one block of them first and bounce it off the top, and in Phoenix Magnion's stage in Z2, off the infinitely rising lava buckets). The manual version can also be used to farm kills in Burble Hekelot's stage for the Defense Form without wasting precious time charging it over and over (on the pair of enemies that jump up from the bottom of the screen together and spawn infinitely, before entering the temple portion).
The antagonists of the first three games in this series all have the Greek letter Omega as their symbol. Sure most of them are Knight Templars, but they still mean well, fighting for the sake of humanity. But later we're introduced to an actual character named Omega, who is everything that the antagonists (except one) ever stood against.
During the Alouette's Good Day audio drama, Rouge and Joan starting going at each other over the names they've chosen for the two baby elves. It's mostly meant to be funny, but during the discussion Joan points out that Rouge's simulation for Operation Righteous Strike would fall apart under even minimal scrutiny. Joan is proven tragically correct halfway into 2 where the entire operation gets every participant besides Elpizo killed, and reduces Elpizo to something much worse.
He's Just Hiding!: Since even official materials go back and forth on whether or not Zero died on Ragnarok and he has a history of doing this, a common fan theory is that he survived somehow. Made even more confusing in Mega Man ZX since Zero does reappear, but as a Biometal. Because of this, it doesn't give either argument anything to work with.
It Was His Sled: Dr. Weil and Copy X's very existences are common knowledge by now. Also, Zero's body being a copy of the original Zero along with Omega's true nature and Zero's Dying Moment of Awesome.
Love to Hate: Ask any of Weil's fans, they'll say how horrifically despicable he is (and how he never suffers Villain Decay unlike previous Big Bads) what makes him such an effective villain. Omega gets this as well, because of his sheer coolness.
"WARE WA MESSIAH NARI!! HAHAHAHA!!"note I will be the Messiah!! Hahahaha! Said by Omega when confronting Zero after the latter learns his body is a copy of the original possessed by Omega.The delivery of the line with the dramatic music is what sells it.
"Megan Man Zero." Once pre-orders for the Zero/ZX Legacy Collection went live, a few fans noticed that physical stores offering pre-orders (with placeholder cases on the shelves) all had the same hilarious typo on the box. People took the name and ran with it.
Alouette, who is ridiculously adorable, and with the chassis of a young child, even more helpless than Ciel.
Moral Event Horizon: Copy X crossed the line in the first game by committing genocide against the Reploids.
Player Punch: Elpizo aims for getting the Dark Elf, and to do so, he had to destroy the seal, X's body. When Zero finally catches up to him near the seal, he forces Zero to watch by binding him with the Baby Elves' powers as he stabs X's body, destroying it and releasing the Dark Elf.
The Mega Man Zero Collection includes an Easy Scenario for players who want to dip their toes into the series' infamous difficulty, improves the music quality to be on par with the DS hardware, allows customization of the controls, and features artworks of characters in the lower screen at appropriate moments (for example: Harpuia's artwork appears when you fight him). The Japan-exclusive E-Reader function is also included as unlockables.
The Mega Man Zero/ZX Legacy Collection has almost the same features as the aforementioned Zero Collection. The lower screen artwork has been reworked into a dedicated Gallery menu. A new Save Assist system is introduced, removing the tedium of losing lives. The Legacy Collection also features original music and remixes of the most iconic tracks of the series, as well as a speedrun minigame in the form of Z-Chaser. Finally, you can switch between the Japanese and Western versions of the games as you like.
Ciel with Zero. Thanks to the large amounts of Ship Tease between them, many fans warmed up to the pairing better than the original doomed Zero/Iris.
Neige with Craft and Andrew with his wife, some of the most blatant examples in the entire series franchise
Some fans ship Zero with Fairy Leviathan. Leviathan's overall rather playful and (later on) obsessive attitude makes it very easy to interpret it as her having a crush on Zero. Dating Catwoman probably helps in this case.
As with the last series, people ship Zero with X a lot.
Saved by the Fans: X. Not from death per se, but from being an Ax-Crazy dictator. Similar to what happened to Axel, this resulted in his inaction with regards to the Guardians' attempts to kill Zero. The sequels give him other things to worry about and the issue really doesn't come up again.
While the Cyber-Elf mechanic isn't bad by itself, the first game punished the player with a lower rank for using them at all despite them being a major selling point. Later games toned this aspect down by only punishing the player for using the more Game-Breaker Cyber-Elves, and finally just giving the player one Cyber-Elf that they can upgrade however they want, and only punishing them for overpowering it.
The weapon proficiency system in the first game is also considered to be a pain. Because of his memory loss Zero needs to "relearn" many basic techniques, such as multiple Z-Saber slashes. This can require many players to level grind just to stand against early bosses effectively. In addition the retry system is also dated due to lives being very rare. Meaning that if you lose all your retries in a level you will need to either start from the last save point or give up the mission, and in the case of the later you don't get your retries back. Thankfully these were both improved upon in the sequels.
While the Form System of Zero 2 is most certainly not this, the acquisition of Ultimate Form most definitely is. Like with the first game's Ultimate Mode, earning it requires you to use all Cyber-Elves by the final boss, and this form is earned upon loading that game's save file. Unfortunately, that means that your Cyber-Elf use from the previous game is carried over, and therefore getting anything higher than D Rank is impossible. Worse, unlike the other games, there is no option to start a completely new game with this Ultimate Form, meaning you cannot have both A/S Rank and Ultimate Form ever, no matter how many times you start a New Game+ from that same file. Only in Collection's Easy Mode can you have both Ultimate Form and a rank above D. This is probably why the requirement for Ultimate Mode in 3 and 4 completely dropped the need to use all Cyber-Elves and simply required collecting each game's respective collectibles (plus fully growing your Cyber-Elf in the case of 4).
Third game: The fight against Omega and The Reveal that he is in Zero's original body, and the ending, specifically X's farewell.
Fourth game: The fight against Dr. Weil's final form, and the final scene, a shot of Zero's broken helmet to confirm his Heroic Sacrifice.
So Okay, It's Average: Zero 1 is considered weakest of the series, although most would say it's still slightly better than just average. Common criticisms include a relatively weak plot and unreasonable grinding requirements for weapon skills and cyber-elf upgrades. Speaking of cyber-elves, the fact that the game's only collectible downgrades the Hunter Rank when they're actually used is considered a Scrappy Mechanic. Overall, the game is hard to recommend stand-alone but is required to play the rest of the series. Thankfully, all of the above issues were improved upon in the sequels.
Surprisingly Improved Sequel: While Zero 1 overall is considered a decent game, it also has its issues both gameplay- and story-wise and many consider it the weakest, not the kind of game that would reach the all-time greats as a whole. Luckily, Zero 2 streamlines the grinding issues Zero 1 has in both Cyber-Elf and weapon skill department, introduces EX skills you could acquire by beating a boss with Rank A or S (thus giving actual incentive to go for such ranks and suffer the wrath of an entirely new attack outside of being a hardcore player), replaces the divisive Triple Rod with a more convenient Chain Rod and includes two additional Sub-tanks meaning you don't have to risk any Cyber-elves and thus lower the rank. It also puts a much larger emphasis on the story and characterization compared to the rather bare-bones plot in Zero 1, something the later games would follow up on and which the series as a whole would be known for.
That One Achievement: Getting 2 of the minigames in the third game requires you to beat the game with perfect 100 points in your average score. This means completing every mission perfectly - complete every sub-objective, beat levels quickly, kill a minimum amount of enemies and take no more than a small amount of damage. Oh, and not using your elves (at least not the Fusion ones) or entering Cyberspace.
Fenri Lunaedge from 4 shouldn't be that bad. Sure, he has an icy floor that can make dodging his wheel jumps a little tricky, but he constantly leaves himself open to punishment from the buster. The fight might take a while because it just simply isn't safe to be next to him and combo him with the Z-Saber (he has an attack with very little wind-up where he just stabs you if you're too close), but it should be easy, right? No. Fenri has two attacks that are pure and utter hell to avoid:
The first, Tenrō Shikku, is described on the actual wiki as looking impossible to avoid, mostly because it absolutely does. Fenri leaps diagonally towards the wall away from him, letting out an energy slash in front of him, before dashing to the other wall unleashing two more slashes, before jumping to the opposite side from where he started while throwing out another energy slash. There is no way a player will ever figure out how to dodge the attack short of looking up a video of Fenri's fight online, because the 'solution' to it is so backwards. You have to dash towards him during the first attack, which looks like it's the absolute last thing you should be doing, dash back, then dash jump between Fenri and the last attack. Good luck figuring that out on your own. You won't.
The other attack is his EX Skill attack, White Fang. It's deceptively simple; he unleashes two energy waves, one from the ground, one from the air. All you have to do to dodge it is climb the wall and then fall. Problem is, falling from the wall can be a little finicky to do given it's more than likely you'll hug it again as you go down, getting yourself caught by the second energy wave. Not only that, Fenri can spam it as many times as he wants - it's not unusual for him to do it three times, and there's no real tell for when he's going to do it again and when he's going to stop.
The worst part about all this is if you fight him at a rank where he'll decide to use White Fang; both Tenrō Shikku and White Fang have pretty quick wind-ups, meaning you need to begin dodging them almost as soon as you see the tell. The problem? The tells for both attacks are almost identical. The only difference is that Fenri will lift his head slightly for Tenrō Shikku. This sounds like it should make it easy to preempt the attack, but in practice the player will be so on edge about getting the actual dodge for each attack done correctly that it can be easy to choke and begin the wrong dodge for the attack Fenri uses. Mercifully, Fenri is incredibly fragile, so if you take out Sol Titanion first you might be able to whittle him down quickly enough to where he doesn't use these two attacks often, and Fenri won't actually enter a stunned animation from getting hit with fire if he's about to use Tenrō Shikku, so that makes the tell a little more obvious.
Aztec Falcon: As he's the second mission boss, you'd be fighting him with minimal abilities (unless you spend a lot of time grinding somewhere else; in Hard Mode, you can't even grind), his boss room is rather narrow, and his attacks cover a lot of space. His wings are also invulnerable, making it harder to hit him when he shoots arrows from his wings.
Phantom is this when compared to the other Guardians. Unlike the others, he's Non-Elemental, thus he has no weakness. You can interrupt most of the other Guardians' attacks; for Phantom, you can only intercept his Dash Attack. He also plays it nasty with said attack - if you jump over it, he'll quickly dash back to you; if you interrupt it, he may sometimes resume the attack. He also has a Doppelgänger Spin attack where, if you hit the wrong Phantom, he'll do a powerful counterattack; he might also quickly dash at you if you're close to the real him. Some temporary phantoms may appear when Phantom is using the doppelganer spin and contact with them causes big damage. During the second fight with him, he has a Kaizo Trap attack should you defeat him. In the secret fight against him in the third game, a number of his attacks are upgraded - his Fuuma Shuriken move shoots spreads of kunai multiple times, and his zigzag floating move has him spamming spreads of kunai while floating. On the other hand, given the secret fight takes place in Cyberspace, where you have unrestricted access to all of your Cyber Elves' powers, even this upgraded fighting style can be overcome much more easily.
Kuwagust Anchus from Zero 2 becomes nigh-impossible on Hard Mode if you have an A or S rank. He moves quickly and his grab moves are hard to avoid, especially one that comes after he sucked you in with his tornado. His A/S rank attack is really hard to dodge: He has to be attacked, in-flight, to avoid taking damage, while you're troubled with the wind blowing against you. You have to attack him enough or you'll eat quite some damage. The game doesn't hint at that at all. Or you can just hit him once with chain rod with right timing to derail his attack, as shown here.
Phoenix Magnion from the same game is also positively confusing. He'll avoid your initial attacks and then counterattack with one of his own, at random. He's fond of Teleport Spam, especially after you attack him. He can only be attacked while he's launching an offense of his own. Worse, the area has "holes" where blasts of magma will shoot out at intervals; during your first fight, depending on which room you're fighting him, the holes are either scarce or covering the entire floor. During the rematch, the design is always the latter one.
Heat Genblem from the fourth game. One of his strategies is to walk slowly towards you, then quickly defends with his shell if you attack. Keep attacking and he'll counter with an Elemental Punch. Another of his hard strategy has him floating next to one of the walls, then firing a continuous laser beam while spinning; you have to follow through or you'll get hit. He's rarely open to attacks, and when he is, you'll have a hard time dodging him to actually attack. To top it all off, thunder attacks (his weakness) are rather weak in this game, due to one of them relying on absorbing shots for its power and the other being a dashing stab, which is worthless against an opponent who's invincible from the neck down. Except... The key flaw in his strategy is that it's completely possible to sting him while he's doing his laser spin, as the open hatch on his body across from where he's firing is totally vulnerable. If you have the Junk set, you can even tear him apart before he can finish spinning in the first place.
Also Craft of the same game; he has a plethora of attacks that will limit your space. Especially, his bayonet attack deals quite some damage if you get hit (and it bypasses Mercy Invincibility, too), and his sniping laser would need a split-second timing to dash under (unless you have the Double Jump chip), and a thrown mine that will give you hell if you don't know you can smack it to detonate it before it splits. He also has an evasion move where he can go through you. In the second fight, his EX Skill is a Macross Missile Massacre that can cover the entire screen unless you can slice a few of the missiles. While it's not a miracle cure for the battle, it is helpful to know that he stands around long enough after his bayonet charge that you can triple slash him from behind, which is notably more powerful than a charged slash. It's a little safer to set your Elf to Hacker-2 so you can use the slightly faster upward slash, and get moving again sooner.
One of the most infamous missions in the series is a Protect the Factory section from the first game. After beating the boss, you need to find and disarm 8 bombs scattered around the level. Finding the bomb locations isn't a hard task by any means, but three of them are placed in a very tricky spot - a section with floating platforms and lots of flying enemies. The main problem comes from the small field of view and inability to look around, all of which leads to constant leaps of faith and mission retries after yet another failed landing. It's also the only level in the game that starts right from the boss fight, which more likely means developers knew that the mission is already hard as hell, so they save players trouble of completing the bomb section from the start after losing the boss battle.
Neo Arcadia Shrine, part 1. The annoying bird enemies are bad enough, but there are also Temporary Platforms that have no side grip, shoot bullets downward, leave no margin for error, and are placed above enemies which you will likely land on should you fall. There's also three bosses: Pantheon Aces, Asura Basura, and Herculious Anchus.
Neo Arcadia Tower due to the abundance of Spikes of Doom all over the level.
Zero 2's Power Room stage, filled to the brim with lava and exploding Telebombs and not much room to maneuver. The stage design is very different from the others, where you have to find 4 chambers with generators; it doesn't have a finish, and you only fight the boss when you destroy the final generator. And to top it off, the boss is an absolute nightmare. Worse still, one of the Cyber Elves hidden here is pure Guide Dang It! material. You essentially have to play Space Invaders in one section, kill every enemy while being blocked by moving platforms that hurt you if you touch them, and after that have to hit the fast-moving UFO in the three seconds from when it emerges to when it leaves.
The Bombardment Aircraft. You start off leaping between moving shuttlecraft which shoot at you while you're using them as platforms, on top of Pantheons shooting at you on top of them, requiring perfect timing so as to not to be knocked into the massive Bottomless Pit. Once past that section, you have to fight a miniboss who fires fast-moving, area-damage missiles at you until you hit it. When you hit it, it drops a row of bombs which can only be avoided by standing exactly where it was previously hovering. Then you navigate through a series of timed stage hazards that will eat right through your tiny lifebar and require expert timing to pass unharmed. Then you have to do a Hold the Line section protecting Ciel for 90 seconds, which counts for basically your entire mission score. If she gets hit, goodbye A or S rank. Naturally, this is a Bullet Hell sequence plus the Pantheons who you have to hit while blocking every bullet. This also ends with a very powerful boss. note It should be noted that the miniboss, a gunship styled after a ladybug, is EXTREMELY weak to Ice, to the point that in not-Hard Mode, it's possible to off it in one shot by using the Chain Rod's charged attack and the Ice Chip.
There's also the Shuttle Factory, which is also long, contains lots of lava and other stage hazards, and a tough boss fight against Fefnir at the end.
They Changed It, Now It Sucks!: Some fans aren't too fond of Zero's new human-like design, or at the very least feel that Omega's final form should have resembled Zero's Mega Man X appearance instead of his redesign.
Even if they chose to abandon the original plan where X was the villain of the first game in favor of having Copy X, they still could have made it so that some of the foreshadowing from the Mega Man X series didn't go to waste. After X4 had Zero be visibly uncomfortable when X wanted him to promise to kill him should he become a Maverick, Zero finds out that the X he will fight is a copy right before the final stage and thus has no qualms about fighting Copy X because he knows that he is not really former best friend, and Copy X freely admits that he is a copy instead of following through with the masquerade that he is the same reploid and using it to try to break Zero. Even then, much of Zero and Copy X's dialogue concerns how Zero feels that Copy X doesn't live up to the original without exploring how the latter is a Shadow Archetype representing a path the real X could have taken (and was going to, which dialogue from the real X confirms was something he was very close to doing after fighting for so long and the reason for why he chooses to leave the rest up to Zero).
Harpuia, Fefnir, and Leviathan all died when Omega's body exploded at the end of Zero 3, but unless the player payed attention to Word of God, they'd assume they simply disappeared with no explanation. All things considered, some believed they should have had a better sendoff, either in Zero 3 or Zero 4.
Tough Act to Follow: Not the games, but the music. The Classic and X series became so remembered by their awesome music that the music of the first game was perceived as forgettable because it could not measure up to those of the other series. The sequels sought to have better music.
True Art Is Angsty: The Zero series is by far the darkest the franchise has ever gone, and yet it's often held up as some of the finest the franchise has ever offered in terms of writing and characterization, with little of the Narm that made some of the attempts in the X series fall flat.
Harpuia's voice is Megumi Ogata, a woman. Plus his name is derived from the legend of the Harpy, half bird, half-women. It does not help that he's wearing the exact same clothes as Leviathan (the female Guardian) with a Palette Swap (what appears to be a midriff-baring shirt and panties).
Cubit Foxtar is based on a Kitsune, which can change genders, hence his androgynous appearance. Curiously, he is portrayed as a female in the original Japanese games.
Anubis Necromancess (boss in Zero 1 and 3) is confirmed to be male. His name in Japan is Anubistep Necromances, with one "s".
Polar Kamrous, despite the matching build and deep voice, is female. Weirdly enough, the Complete Works book refers to Kamrous as male.
What Do You Mean, It's for Kids?: The entire series qualifies, for the reasons listed on the Nightmare Fuel page for the entire franchise. There's also the fact that the Neo Arcadian government basically does a systematical genocide on Reploids to solve energy crisis. And the game was rated E in its original release (it was bumped up to T with the release of Zero/ZX Legacy Collection, most likely due to inclusion of the Japanese versions, which had bisected enemies bleed out red oil).
Win Back the Crowd: The first game impressed after the disappointing Mega Man X6, and the Zero series continued to improve while the X series declines even further with X7.
Ciel. In two separate occasions, she thought that she was doing the right thing, but it only ended up giving rise to worse problems. The first one would be for creating Copy-X, who went insane and started a genocide against the Reploids. The Resistance is partly her effort to make amends for what she's done. The second time was successfully researching an energy source that she believes would put an end to the war, only for it to be a catalyst to a new conflict. Mind you, this is a person who longs for peace as much as X, and she is very young at the series' start, and also human. And, then there's the fact that, at series' end, she is waiting faithfully for Zero to come back, when it was completely impossible.
Alouette is implied to have gone through a Break the Cutie livelihood, and might have suffered even worse, if Ciel hadn't found her.
X. The only cure for the virus that they had worked tirelessly in looking for for well over a century is weaponized into a living maverick-maker. His best friend's body is stolen and converted into an ultimate weapon that wipes out most of the planet's already-perilous population, with Zero going into an intended-eternal stasis, leaving X with basically no shoulder to lean on for moral support. He's forced to manage the virtual entirety of the world's remaining population and all maverick activity by himself and effectively kill his body in order to seal the aforementioned corrupted cure which not only leaves him off, but his soul is then split into fifths. X is forced to watch as the Copy made to take his place ruins the haven that he had so desperately fought to create and preserve and his "offspring" are then tricked into being assassins and strongarms for the sociopathic copy. Finally, X is murdered in his comatose state by a villain who just wanted the Dark Elf in a screwed-up and misguided attempt to save all reploids from further retirement and destruction. X did not even get a chance to fight back against his assassin. He finally spends the rest of the following game slowly, slowly dying and using every precious ounce of power for the sake of others.
Almost all the tragedies in the X series are inflicted on Zero, and even more are piled on here. Like the fact that he wakes up seeing the current state of the world, and freshly awoken, he has to continue fighting, again, and he was able to finally return the world to a peaceful state, which was what he and X have been fighting for a long time, only for him not to see it come to fruition, seeing as he's dead...
Woobie Species: Reploids, who are subjugated and oppressed by Copy-X's forces. By the start of the first game, countless Reploids have been unjustly branded as Mavericks and killed to preserve power for humans.
Woolseyism: Some of the boss names are changed overseas. In particular, Dr. Weil's name was originally Dr. Vile. There's already another guy who's named Vile (who is originally called VAVA), so the name change is to avoid confusion. If pronounced in German, it can still be read as "vile". There's also the fact that it's quite meaningful in its own right (being the Big Bad, Dr. Weil is the Dr. Wily of the Zero series).