Zero's decision to kill Weil seems to be spitting on the laws of robotics that were so important to the series. However, his decision is in accordance to the Zeroth Law of Robotics, which in essence is a threshold law designed to protect the human race, as obeying law 1 would cause humanity to be harmed through inaction. It's made especially ironic given that Zero was never built with the laws in mind (Wily made him and all, and he's technically a "Robot Master"), yet he unwittingly follows the most important law.
Another possibility is that the Zeroth Law doesn't exist in-universe: one can argue that letting Wily live endangers humanity thru inaction. Alternatively, it does exist but it wasn't until Zero 4 that it could actually be applied: Wily isn't an active threat when he's defeated, nor was Weil in the backstory. But Weil became an active threat when he fused with Ragnarok.
Weil is also a mass murderer despot. The spirit of Law Zero was intended specifically to stop people like him (think of Adolf Hitler and Pol Pot), and will override the first law.
All of this comes up because Weil himself brings up the topic, that Reploids like Zero should serve, and never harm, humanity. It basically blows on Weil's face due to the Zeroth Law.
Also, Dr. Light's dream was for humans and robots to live and treat each other as equals. Zero treated Weil like any other Reploid he's fought, demonstrating that equality. He even outright calls him "just another Maverick," a term which up until the fourth game was used exclusively for Reploids. This also explains why it fell to Zero to realize Light's dream: for all his talk, Light subconsciously did still put human life higher than robots, hence Rock being Three Laws-Compliant and X's 30 years of testing. If he had accepted that there are times to kill, Dr. Wily would've been picked off before Zero could be built, preventing so much pain and suffering.
Speaking of which, remember the ending of Mega Man 7? Wily got away because Mega Man couldn't follow the Zeroth law. Then he went on to create the Maverick Virus, and you know the rest. By following the Zeroth Law, Zero was able to do what Mega Man could not destroy the villain and create an era of peace.
Then again: since so much of Weil has been Mechanized (even to the point that they digitize his mind so that he'll forever reflect on his sins), it's hard to argue that he's human anymore; hell, at this point he's might as well be the last legit Maverick that Zero ever fought.
The final battle with Zero and Omega Zero can mirror the fact that Zero is fighting his old self. Remember that in X2, Sigma made reference to Dr. Wily for Zero being his last creation. In X4, we know who the silhouette is in the beginning of Zero's nightmare. And X5, everyone obviously knows, but Sigma does not refer to him by name to X and Zero. Also, Zero was Ax-Crazy within Sigma's flashback. All the plot build-up from the entire X series to Zero 3 makes a true resolution of the story of Zero finally taking down what represented his evil side. And since Zero lost his original body, Dr. Wily's final creation is technically destroyed, but the original Zero's mind still exists.
Why doesn't X show up in Zero 4? He's finally dead. In Zero 2, his physical body's destroyed, and in Zero 3, he leaves Zero to return to Cyberspace.
The Japan-exlcusive e-Reader cards also appearing in the Compilation Rerelease on the DS (this time in all regions) includes a poster of MegaMan.EXE alongside a poster of Ciel. It may seem a bit of a stretch, but both of these series were released around the same time and were the first two series to finish their storylines. Another thing they have in common: Cyberspace!
This may count as Fridge Heartwarming: At the end of the series, Zero is dead and is supposedly in Cyberspace. Fastforward to Project X Zone, Iris is brought back thanks to the representatives of .hack. Now, what does .hack have in common with the Mega Man series? Cyberspace. Zero also vows to find Iris once again. So, in essence, at the end of the series, Zero and Iris are finally reunited.
In the manga adaptation of the first game, Copy-X (here called the "Perfect Reploid") is a fusion of the Four Guardians created by Ciel's younger sister, Cial, rather than a copy of X himself. It may sound crazy, but the Four Guardians were made from four pars of X's DNA in the series.
Of course the Proto Form/Junk Armor would reduce your defense. Word of God says it's the Black Zero armor from the X games. Where does Black Zero appear the first time? At the end of X2, when it was easily destroyed with a single slash.
Due to Copy X's nature, he was doomed to go crazy. When Copy X finally meets Zero, he freely admits that he is a copy of the original. But how exactly did he come to this conclusion? Everyone believed him to be the true X, except for Ciel. Imagine how his life would have been ever since he was born; he's activated as a newborn reploid with the experience of a child, but everyone around him believes that he's their beloved X come back to them. Already, he's had an impossibly heavy mantle of expectations hefted onto his shoulders before he even really knows what's going on. So he tries to fit into these large shoes and be the 'X' they want him to be after all, they say he's X, so he must be X, right? But...he doesn't have any of the memories or experiences of the original X. Eventually, he comes to the only real conclusion; that he's only a copy of the original. His entire life is based on a gigantic lie. If everyone knew the truth, they would abandon him, because he's not the X that everyone loved and respected. He, understandably, suffers a psychotic break. It's at this point that he begins his campaign of iron-fisted rule, because if he can't be the beloved X, then he has no choice but to be better than him in order to earn that love by his own merits. Copy X might be a cruel tyrant, but his upbringing really didn't leave any room for anything but an unstable, emotionally skewed individual. Bonus: he wasn't put into 30 years of morality testing, unlike X. He really doesn't know better about the right thing to do.
In the first game, you're sent to retrieve data from the intro level. When you get back with it, Ciel laments that aside from the Triple Rod and Shield Boomerang blueprints, most of the data was corrupted and useless. It was in a server in Maha Ganeshariff's body. Maha Ganeshariff's elemental weakness was the Thunder Chip. What happens to data when the server it's stored on gets zapped by lightning multiple times? It was also in the underground lab Ciel found Zero in, so that data probably included backups of Zero's memories, in addition to blueprints for his weapons. So this mission might also be why he never completely recovers from his Identity Amnesia.
Adding to this, Maha Ganeshariff's weakness to the Thunder Chip might seem odd due to him being a Non-Elemental boss...until you notice he's fought in a room full of knee-high water.
The low-orbit spaceship that Omega was exiled to is shaped like a sword. Omega was an almost literal Sword of Damocles hanging over the head of Neo Arcadia.
In the fight with Phoenix Magnion, the appearance of Colonel alongside violent Mavericks such as Vile, Agile, and Bit initially seems odd. Until you realize how draconian Neo Arcadia has become; if theyd label someone like Alouette as a Maverick, they would of course lump Colonel in with those sorts of crooks!
The battle with Omega at the end of the third game can be a bit of an Anti-Climax Boss, given that for his massive pool of moves that can potentially be quite dangerous, a properly-upgraded and prepared player can potentially take him down in less than a minute. But this makes sense for two reasons: one, both Zero and Omega are wielding Z-Sabers, which have rendered short work of just about everything else, so this turns their climactic duel into Rocket-Tag Gameplay. And two, besides all the EX-Skills and chips he can acquire, including one that lets him phase through attacks, Zero's memories and experiences grant him a significant advantage in precision and effectiveness over Omega basically jumping around and blowing everything up recklessly - after all, Zero in the copy body beat Omega once before alongside X, and that was when he was fresh to that body.
Players new to the Zero series may wonder why charged shots and sabre slashes do so much damage to bosses (chopping off a good quarter of their life bar), in comparison to the X series, which may see, at most, three or four ticks off of the health bar at best. A clue might be found in the design overhaul the game took - by getting rid of the bulkier designs (such as the heavy armor and huge metallic boots), the Reploids have effectively traded defense for a slimmer, more streamlined design.
Why does "Fate ~ Theme of Weil" play before every boss in Mega Man Zero 4? Because these are not just any old Mutos Reploids; these are the Einherjar Eight Warriors, an elite squadron of Neo Arcadia's most fearsome soldiers. Many of them proclaim their loyalty to Weil specifically in pre-boss dialogue, and they are all eager to see Ragnarok destroy Area Zero. Unlike previous series bosses, who had a wide variety of motives and loyalties, and the Einherjar are true extensions of Weil's cruel will. (with exception of Tech Kraken, who merely wants to avenge Phantom).
The forgotten laboratory, where Zero is found and resurrected as well as the final stage of his fight against Omega, is in complete and utter disrepair. Considering canonically that Zero's data was expunged from the records so he wouldn't be found, that's one thing, but the place was also the origin of Cyber-Elf research — and where Omega was created, and likely the Mother Elf's corruption into the Dark Elf. Even if the facility was damaged and abandoned from the Elf Wars before Zero sealed himself there, it also doesn't explain why he's so tattered and torn up that it took Passy's Heroic Sacrifice to revive him. What in the hell happened that Zero's own resting place looks like an apocalyptic bomb shelter rather than a proper research facility?
Omega, the Ax-Crazy psychopath whose Hate Plague powers and ceaseless thirst for blood that ended up killing 75% of sentient life. The horror kicks in when you realize that Omega was exactly what Dr. Wily intended Zero to be. In fact, given what happens in the whole timeline, actually letting Dr. Wily win seems to be genuinely preferable to just thwarting his plans. As bad as his schemes got, they never went as far as what Sigma or later villains wanted.
Remember, Wily became evil because his pride was hurt. Meaning if he won, it would be more or less just to prove he's better than Dr. Light. If he won, mankind would probably just have to deal with his ego for a couple decades until Dr. Wily dies (he's already quite old). Compare that with the nigh-undying Sigma and DoctorWeil, and you'll be rooting for Dr. Wily in no time.
Think of the attitudes humanity has towards genuinely non-violent robots: in 9, we see the Robot Masters are still online when Wily finds them. In X6, Gate's Reploids are killed off due to their potential risks instead of merely reassigned; in the context of this series, robots are basically sentient, so humans are willing to leave living people to basically starve to death, or outright kill them, out of convenience. Yet, people like Dr. Wily and Weil get to live, with no "kill on sight" orders established before being captured. How horrifically skewed are humanity's priorities towards robots and humans to even allow this to happen? The worst part about this? This means that Dr. Weil's Breaking Speechhas ground. Only humans understand the joy of power, indeed.
Even worse, the Official Complete Works states that it was the Eight Gentle Judges that Weil created who sentenced him to exile. Humanity not only didn't have it in them to pass judgement on a fellow human for his horrific crimes and left it to the Reploids to solve for them, but they gave his fate up to something he could easily have manipulated, to which it's stated he did. They basically handed Dr. Weil his long-term revenge plans on a silver platter by giving him the perfect out to exploit, because no one wanted to take responsibility or charge on any of it. And yet they put him in a regenerating armor that kept him alive, just so he could die over and over again to suffer for eternity, not only justifying said vengeance further but showing a gross incompetence for immortalizing a madman and an almost petty and vindictive attempt at punishment only humans could have chosen to inflict upon another human... the exact thing Weil attempts to do in Zero 4 by giving humanity a slow, torturous extinction. Weil is a monster of his own making, and yet humanity's decisions in regards to him only help reiterate that he's the worst of a complacent and vengeful humanity.
Speaking of a monster of his own making, the entire reason Dr. Weil caused the Elf Wars in the first place was because of his indignant anger over the Reploids getting a slap on the wrist because the Maverick Virus was cured. While not wholly justified, given the nature of a corruptive computer virus that makes one Brainwashed and Crazy versus the ambiguity with someone claiming they were Just Following Orders, it also means Weil himself had vindication, as he was likely only one of many humans enraged about the aftermath of the Maverick Wars, and the persecution of Reploids in the Zero series' present only further proves him right. And as the villains of Mega Man ZX would go on to show, there really would be more people willing to commit atrocities in the name of what they believe in; Weil may be the absolute worst of the Mega Man franchise, but put anyone in his shoes and the series goes to show that any human could become another Weil.
Weil's "warning shot" with the Ragnarok was the only reason Zero & co. were able to defeat him. If Weil had just kept his mouth shut and improved his aim (which he had plenty of time for, since he was presumed dead from the destruction of Neo Arcadia), he could have used that shot to annihilate Area Zero or the Resistance base where Zero and Ciel were at the time. That's right, if it weren't for the Villain Ball, Weil would have won, right then, right there, with nothing you could do about it.
From the manual: Weil was among the scientists who tried to resolve the Maverick Wars; specifically, he and his colleagues studied Zero's empty body. However, while Ciel's ancestor studied Zero's cognitive program for a cure, Dr. Weil viewed Zero's body as the ideal weapon to end the wars and used it to develop Omega, while Ciel's ancestor created the Mother Elf, which would be used by the original X to purge the Sigma Virus for good. Dr. Weil then proposed Project Elpizo, a plan to combine the Mother Elf with Omega to exert control over all Reploids. This put Dr. Weil at odds with X's ideals of coexistence between humans and Reploids. Undeterred, Dr. Weil placed a "curse" on the Mother Elf that turned her into the Dark Elf, and created clones named Baby Elves to control Reploids and make them fight each other in a massive battle royale. The panic and destruction caused the people to favor Project Elpizo, but X and Zero (whose program was put in a new body) recaptured the Dark Elf, forcing Dr. Weil to unleash Omega in the battlefield. Omega would move on to slay a large number of humans and Reploids before being finally defeated by X and Zero. Omega was sent away to Earth's orbit in the Forbidden Ark, while a group of humans converted Dr. Weil into a cyborg and cursed him to wander the wastelands of Earth as punishment for his crimes.
Now remember when he said "I am The Devil"? Now consider these: Being one of the good guys at the start? Check. Being envious to one of the good guys that solved all the problems? Check. Cursing the tool (i.e the Mother Elf) that was previously used for peace, and created an Antichrist to wreak chaos, just to spite said good guy? Check. Being banished to "hell" after all he had done? Check. Falls from the "heaven"likelightning? Double check. Said good guy sacrificed himself to stop the whole mess? Check. Now sum them up, and then you'll think of him as Lucifer, a.k.a. the Devil itself.
Because of the destruction of Neo Arcadia, where else would the Resistance take the survivors but to Area Zero? (The presence of Colbor, the leader of the rescue team, in the Caravan's campsite during the ending supports this logic.) If so, then Weil's Colony Drop wouldn't just destroy the environment and those dissidents in the Caravan, but probably also result in an instant Kill 'Em All. So much for a slow and painful death as Weil wanted the Neo Arcadians to go through.
The fact that the rank-and-file Pantheon troops look like Cyber Cyclops versions of X. Zero spends three games butchering robotic mockeries of his best friend en masse.
Concept art shows that at one point in development those cyclops eyes were mind-control masks placed on unwilling Reploids to make them loyal soldiers. Yikes.
The Retirement Facility is already creepy enough with dead Reploids everywhere, but once Weil takes over, theres probably also bloody dead human remains in there too.