Mega Man Zero/Headscratchers

How in the name of all that is holy can a totalitarian, oppressive, racist and despotic military state ruled by an iron fisted fascist dictator who has had countless innocent men, women and children brutally slaughtered for the most minor of offenses be constantly praised as a utopia? Is humanity just stupid and/or blind to Copy X's atrocities?
 * I think its mostly desperation. Remember that this was a Crapsack World at its absolute worst before Copy X started getting over the top. After a century of things going from "apocalyptic" to "are we dead yet? No? Darn." and further, a society not under constant assault by mavericks, with enough food and energy to meet basic human needs for health and a small measure of comfort, a stable location enabling fortification and emotional attachment to place rather than the nomadic lifestyle a broken world full of mavericks and scarce resources necessitates, and a sense of law and order rather than the worst kind of anarchy must seem so amazingly wonderful that they can't think of any other word for it.
 * It's a utopia for humans, and that's really all that matters to Copy X. Reploids are pretty much outta luck, but those living in Neo Arcadia don't care. They're Mavericks as far as they know.
 * Humans Are Bastards. Or, at least, perfectly covered by The Masquerade that they seemingly don't care. Until in Zero 4 where we see actual human refugees from Neo Arcadia; they said that they're tired of all those wars, and that they suffer while the Reploids just battles in their stupid war (at least after Weil's dictatorship starts).
 * Also Remember that Copy-X wasn't the ruler of Neo Arcadia since day one, in fact, he was only ruler for 8 Years (was build by ciel at Age 6, and she was 14 by Z1) so it was the Real X the one on charge, he ruled for almost a Century, and we know he always wanted peace, so i doubt he was a opressive ruler, and even when Copy-X took his place he continued Pleasing the humans at the expenses of the reploids so, at least for them, it was still being a utopian society ruled by the Wise and Noble Master-X.

Why would all the bosses have the Omega letter as their symbol, considering the obvious implications?
 * The Omega symbol is supposedly Neo Arcadia's symbol. Now, why they adopted it is another question entirely.
 * Neo Arcadia is probably the last metropolis on the planet, since it is one of the only inhabitable areas left, and is described as a human utopia.

Why is Zero's resting place still accessible in Z3, when it very clearly collapsed during a mission in Z1?
 * That's one is easy to explain. It's apparent that Weil cleaned it up, seeing as how his base is suspended above it. Presumably he just did it for dramatic effect. A better question is how light was streaming into it in Z1 when it's shown to be underground in the same game.
 * Alternatively,  opened it back up. As for the light, maybe the light was artificial, or it wasn't deep underground.
 * Maybe Weil left the lights on in Z1.

Roughly half of the ice-elementals in this series are fought in Underwater Boss Battles, yet it doesn't dispel their weakness to fire.
 * It still inflicts intense heat damage.

Why didn't they just execute Weil?
 * Probably for the same reason they didn't execute Dr. Wily for all the crap he did before Mega Man 7. I can only imagine that humans in this world didn't want to consider the implications from properly punishing a human that was arrested by robots, preferring to just brush the problem aside and not dealing with it.
 * Given that Weil's Numbers are former judges, it's heavily implied that back when he was sentenced, he had enough control of the courts to prevent execution, or some other effective punishment.
 * Actually, Zero 3 heavily implies that Weil's punishment was actually done outside the law (Copy X said that it wasn't done under normal regulations and unlawful), and Weil's reaction and rant indicated that his punishment also had him extremely POed at everything. Although control over the courts was correct, as a later pamphlet revealed that the Eight Gentle Judges were actually originally created by Weil.
 * But then again, Copy X is possibly reprogrammed by Weil, as he becomes even more ruthless than he already was in the first game. So the punishment being under normal regulations and unlawful is possibly a farce.
 * Possibly reprogrammed?! The dude went from doing whatever it took to protect the humans to being totally okay with Weil launching a missile at a residential area! Not to mention the fact that he was resurrected by Weil...
 * The fact that Dr. Weil himself says "And Humans! Look what they did to me!" indicated that the punishment that Weil received was definitely not what he wanted, so most likely this was not the result of it being a court decision.
 * It could be - seeing that the courts are made from the Eight Gentle Judges, who are made by Weil; it's not hard for him to manipulate them into giving him a less severe punishment. Maybe the humans went mad of that injustice and then decided to go vigilante on him, giving the immortality suit and whatnot, outside the laws.
 * Also note that the humans of that time wanted weil to suffer a Fate Worse Than Death due All of his crimes, and what idea did they come from? seal him on a prission on the middle of nowhere, unable to do anything for all eternity, but as we know, he was able to free himself, and he was quite pissed about the whole incident.

Just where did it hit?
 * Possibly nowhere, from the image shown when he fired it.
 * Which only leads to more horror. If Weil had slightly better aim and hit either Area Zero or the base where Ciel and Zero were at the time, the game would have ended right then and there, with nothing you could do about it.
 * Well, considering it can, the effect could have been devastating if done to Area Zero or the Resistance base (or even both at the same time). Emphasis on "could have been."
 * Oh, I don't think it's a Villain Ball. Dr Weil is both egotistic and intensley sadistic. He likely made a "warning shot" to terrify the people, leading them up to one enormous and painful Despair Event Horizon. Let's face it, he'd be in to that sort of thing.

So if Omega was so powerful 100 years ago that it took the combined efforts of X and Zero then how is it possible that Zero is able to so effortlessly take down Omega in all 3 of his forms, the armored shell, the Omega X and Zero exoskeleton, and Zero's original body which were all augmented by the Dark Elf? You mean to tell me that Zero is more powerful than X and Omega ever were after having been in hiatus for 100 years? X having been active for about 90 of the 100 years that Zero was asleep (X was sealed 8 years before the events of Zero if I recall correctly) should have become so much more powerful than either Zero or Omega ever were that handling the Dark Elf's release wouldn't have required the use of sealing it in his body but rather be able to stop it outright. As for your original question, it can be said that, right, Zero's new body is indeed stronger, but what really kills Omega is Zero's natural skills and determination. And Gameplay and Story Segregation.
 * As you said yourself, X might be powerful, but he's just a Cyber-Elf now. Not to mention that his body is destroyed in the second game; it's said in the manual that said body is important in keeping his energy and powers as an elf. Hence him being exhausted and his death at the third game.
 * You have to remember X is a robot, a machine in use for many years suffers a great deal of wear and tear, so its possible he was weakened.
 * Zero only wounded Omega to the point where his recovery systems would kick in and undo the damage. It was only because of the help of the guardians that he was able to finish the job. And it's possible that, not having any other help, X and Zero did resort to the Final Strike to take him down because there wasn't anything else capable of doing it at that time (not to mention that at that time, they were against numerous foes, and not just Omega, so it's possible that their choice of attack was meant to defeat everything at once). After 100 years, even in a Crapsack World, weapon technology might've progressed enough so that Zero would be able to deliver an attack that strong. Besides, Zero is a Determinator, and even with the Dark Elf's enchantment, his power is pretty similar in level to that of Omega (not to mention the fact that in every fight he is in, he defeats superior foes purely because of his skill).

How do you pronounce Ciel? Seal, Shell, Kee-el? I know SNK vs. Capcom badly translated her name to "Shell", but still...
 * The name is in French, so you might want to take a look at French pronunciation. But the word with the closes pronunciation to it in English is "seal" (it's something like "see'el", to be exact).
 * From what I saw around the net, the pronunciation of the french word is "See-elle", so I think that is the correct pronunciation.
 * Two syllables: "see-elle" is correct. Think of the two letters C and L.

Of all the pictures of Zero they can use (there are a lot of it in this very series, after all), why use for Alouette's/Prairie's Precious Photo gallery in her room?

According to the backstory material, normally only Reploids can see Cyber-Elves. However, we do see some Humans interacting or reacting to them and know about other cases of Humans interacting with them from the backstory. Now most of these cases are explainable,(Ciel has an innate abilty that allows her to interact with them, the creator of the Mother Elf is Ciel's great-grandmother, so she probably had that abilty too, the humans of the ZX series have mechanical implants, and Post Elf Wars Weil has a mechanical body.) but what about Wiel before he got the mechanical body? He was able to corrupt the Mother-Elf, so he could probably see her, and it seems unlikely that he had Ciel's abilty, as while it would help explain his Reploid revival speciality, it's explained as some sort of an empathic connection, which doesn't seem like something somebody like Weil could have.
 * The manual states that Weil is one of the results of an experiment that gives birth to Ciel: humans with an ability to interact with elves. So yes, Weil can naturally do it before he got mechanized.

Why do people WANT to insist Zero 3 to be the true intended finale (because of the insistence of What Could Have Been)? It's like they even wanted the fact that Weil is still alive at the end of the game.
 * From a thematic standpoint, it works well enough - the Book Ends with the abandoned lab, Zero confronting his original purpose, Zero and the Guardians working together to finish a job from a century ago, X committing the world to Zero once more before passing away, and the fact that Zero's last words in Zero 3 are "I am Zero", something that people have had to repeatedly tell him over the last two games. As for Weil, there was an implication (ultimately unfounded) that Weil couldn't rule Neo Arcadia without Omega. I like Zero 4 myself, but it can't be denied that there was no way for it to continue the Elf Wars arc and that it has a different conflict from the previous three games.
 * You never answered WHY the FANS wanted Weil to be alive.
 * It's not that the fans explicitly wanted Weil to be alive; they just don't care if he's alive or not. This troper has seen some theories on how ZX can go without him dying (at least in the games), or how an "alternate" Z4 can go.

If Omega is Zero's original body, why doesn't he use Zero's X design? Even if it can be Handwaved as being because of the art style, that's a pretty big change.
 * Actually looking at Zero's character design Zero doesn't look that much different from his original appearance (the face and hair doesn't look vastly different to the point you can't tell that it is really Zero) aside from the armor, this can easily be justified in-story by saying that some time during the Elf Wars or maybe even before that point he decided to replace his bulkier armor with sleeker and more mobile armor.
 * Except that Zero already had his new body during the Elf Wars. He sealed himself in the final cutscene of X6 (which according to Word of God is set some time after X8, to purge the Maverick Virus from himself. His body was used to create Mother Elf, a vaccine for the Sigma Virus (presumably killing the Big Bad off once and for all). Dr. Wiel stole his body and Mother Elf, and converted his original body into Omega. Zero was given a new, upgraded body and sent to fight Omega, and sealed himself after the war ended because he was tired of fighting and because, to quote the Mega Man wiki, "as long as he was still around, the bloody history would repeat itself over and over again." So in all likelihood Dr. Weil is responsible for the differences between Omega and Zero's original design, and Zero's new body was likely based on Omega's appearance.

Why should Zero's mind not being in his original body even matter? Zero's body had been blown in half twice in the Mega Man X series so there is no way that half of his body is still even "original" to begin with, and on top of that even sentient machines would need to have older parts replaced with new ones over time getting rid of any semblance of an "original body". Furthermore the idea that for androids all they have is their bodies is blatantly untrue (as one member of the Resistance stated his opinion to Zero), their minds are composed of data and this data can be transferred and moved out of the body, that applies to humans as our brains/minds cannot be moved out of our bodies (save religious perceptions of a soul existing). Zero himself didn't seem to be bothered by this but people around him seem to make an issue out of it when it really isn't one.
 * Note that the people making a big deal out of it are Weil, X and the Guardians, and Ciel. Weil is after power, which one would assume to be a physical attribute, and in any case he has a good motive for trying to Mind Screw Zero. The others seem to be more concerned about how Zero would take it, rather than believing it's actually important. (This is a valid concern - since Zero can't remember anything from before his unsealing, for him the logical leap from "My body is a fake construct" to "The data forming my mind is a fake construct" is not that great.) As for the importance of having the original body, the first time he was blown in half, he was repaired by Cain or Serges (who may or may not be Wily) and the second time, one of the doctors was probably involved. So the repairs would have been done to the same standard as the original. In contrast, it's never made clear what went into the production of Zero's clone body.
 * On the contrary, it is implied that Zero's current body is inferior in terms of overall quality of construction than his existing body. Also, Zero has been having something of an identity crisis for most of the series thus far; something that was once part of (or belonged to) the "real" or "original" Zero would be an object of great significance to him, probably in an attempt to reconnect with his past self and memories if possible. It may not make as much logical sense, given that he's not human, but the Reploids are repeatedly shown to be pretty human-like in their thinking. This Troper interpreted Zero's destruction of his old body as a statement of his identity entirely independent of any container (original body or otherwise), and an assertion of who he is.

OK it is certainly a fair question to ask why Omega and Weil weren't executed after the Elf Wars, but a question that is never even brought up is why they didn't put Zero's mind back in his original body. After the Elf Wars Weil was banished into the wasteland his war had created left to rot for all eternity and Omega's remains were shot out into space; however did no one think that maybe they could purge Omega's mind from Zero's body and give it back to Zero? Weil is left without the use of Omega as his personal God of Destruction and Zero gets his body back.
 * I think that Zero never wanted it back to begin with, given that he sealed himself out of angst at all the bloodshed he was directly or indirectly responsible for.
 * I objected at the "angst" that you brought up; he's never shown angsting, at least in the audio drama. But the rest are right. As for the question itself, maybe the better question will be "why didn't they separate Omega's mind from his body?" Zero didn't need said body, as you said before.
 * I assume that they never figured out a way to subdue Omega long enough to actually do that. As for "then why not destroy the body and the mind?" my fanon is that some people (doesn't matter who exactly) thought that killing Zero's body would also kill his mind, as is the case with armour-bound souls in Fullmetal Alchemist. (In Z1, after Ciel meets Cyber X, she deduces that his body is still intact, which is a strange logical connection to make if such a rule was not believed to exist.) This turns out to be false, but it's enough that someone believed it at the time.

Was Zero successful in purging the Maverick Virus from his original body? If not, it would offer an explanation that Omega is his original self reasserting control after the goody-two-shoes personalty was removed.
 * His original body is said to contain some residual viral data (from which the Mother Elf is reverse-engineered), so it could be a valid explanation. However, his original self (the one you see in the X4 flashback and in X5's bad scenario) is made of both Zero's AI and the conglomeration of viruses; since Zero's AI is extracted out, the things left are said residual data and the Dark Elf (when the Zero Virus going full circle) which are then used to construct Omega.

Wait...so having Ragnarok crumble and explode is enough to wipe out Dr Weil, but a full blast from said weapon, capable of destroying an entire nation, only scratches him?
 * Well, he could only "die" because he integrated the whole Ragnarok system into him; it became the extension of his body. By destroying Ragnarok, he got shut down.