I've got a similar thing simultaneously on DeviantArt. Anyway, to the matter at hand we go. I'm sure anyone who's seen Mega Man Zero knows the story, which should have more roots to the X series just as it should do the same with Classic might I add. After the destructive Elf Wars that nearly destroyed Humanity and all Reploids, Mega Man X organizes his Neo Arcadia organization into a city-state under his leadership which lasts for at least 92 years or so until he gives up his body to enforce the Dark Elf's seal and his DNA soul splits into his Cyber-elf and the Four Guardians. That's when others in power have genetically modified child prodigy Ciel create a perfect replacement for their master.
Alas, without the ethical testing, experience, and full understanding of the world that the true X had, his copy decides to place more value over the Human citizens over the Reploids during an energy crisis which leads to the city's destruction at least 9 years later after his battle with the Resistance and being usurped by Dr. Weil.
However, there are a few things I'm sure many have been wondering. Why did Copy X, a full on Reploid, discriminate against his own kind while allowing a good chunk to serve as his soldiers and judges? Why did the Humans ever doubt that his claims that he couldn't be a Maverick. There are a few other questions I can think of, but can't find the words. However, I think the real reason isn't as simple as Capcom showed us.
Lately, I've been thinking that Copy X's actions, regardless of his loyalty to Humankind and his naïve mindset, were more Machiavellian than people gave him credit for. Think about it. In such a society, it would be most likely that a cult of personality would be formed around the original X's image and deeds which his copy would take to heart. From what I gather, there are examples both past, present, and fictional of people idolizing heroic-looking individuals as long as they both believe and get something out of it. In this case, Copy X gave the more easily placated Humans more essentials and rights for them by giving the more questioning Reploid civilians less room to prosper.
Of course, not any Reploid was randomly labeled a Maverick. I believe that among the Neo Arcadians who would hold some reserve to the X cult, Reploids would be the most likely to have a growing number for that just as Copy X would believe them to be more energy consuming than Humans as they are a machine race that run on energy, and with him being a complete perfectionist, he'd desire Reploids smart and strong enough to keep Neo Arcadia secure and stable, but not to the point that they could overthrow him. Therefore, with the right means, he schemed to concentrate the more potentially rebellious and threating of the Reploids as easily disposable, yet workable, Mavericks while the more fitting and loyal were placed in his armed forces with the Pantheons as his non-sentient foot soldiers as a similar situation occurred to the Human citizens. No matter how influenced he was by Weil, he did bomb a Human district and accidents can happen. Hence, by the first game, Neo Arcadia was a Human-centered and Copy X loyalist-dominated society.
I know it's all speculation thought up by my brainwaves, but I think it's very plausible. Bottom line, while Copy X did create a Human utopia on the bodies of his own kind, I believe he was just as taken in by the trope "Despotism justifies the means". Thoughts?