My best guess would be that Copy Chip production, being a very significant and very complex undertaking, was originally classified and remained so until sometime between X7 and X8. Nothing in X7 says that Axl is the prototype for a new line of Reploids, that knowledge didn't come until X8.
Where did it prove that? Sigma says he had his own data engraved on the copy chips, but nothing in X8 says that the Sigma data in the copy chip is Sigma's data without any of that viral influence at all. The opposite, the ultimate destroyer's DNA contribution is highly credited.
But how does Sigma's DNA, which is to say the X1 body's DNA, relate to the virus? That Sigma tampered with Copy Chip production is his own statements, that he would have tipped the scales in doing so is a reasonable assumption, but that in and of itself doesn't necessarily denote a virus-related strategy. Sigma's no stranger to other means of coercion, as we've seen in X4 and X7. Selectively choosing which enemy gloating to accept and ignore hardly justifies the position, either.
It's also incorrect to assume that the X8 Mavericks have no reservations about what they're doing. Confront Dark Mantis as Axl sometime, he admits to being jealous of Axl's innocence.
Speaking of Axl, one has to ask how he fits into this. Where is the line drawn between Axl and the finalized New Gens? If the cause of their Maverick behavior is viral, is this to say that Axl, the prototype, has greater antiviral abilities than the finished models? Lumine, when asked on this topic, responds with "Sorry, but prototypes like you don't have the specs to pull something like that." Most all of the New Gens and Sigma are well aware of the fact that Axl has no potential to join them, so why?
The primary difference between Axl and the finished New Generation Reploids is that the copy ability was perfected. It's not so far a stretch to think that Axl's limitations (prior to Command Mission, anyway) are what denies him the ability to achieve the likeness with Sigma that the other New Gens do.
There is such a thing as one who goes Maverick of their own accord, as Sigma outright states in MHX when he releases Vile. So the possibility cannot be denied, and the idea that Vile would share that theme with Sigma, Lumine, and the New Generation Reploids goes a long way to explaining his presence in X8.
It's mentioned many times that Zero had the potential to be like Sigma and join with the New Gens as well. Why? The virus. Or rather, Zero's original programming. The removal of inhibitions, the desire for the purity of destruction. To become a new world's messiah, Omega might say. But our Zero rejects that path, and so must be destroyed as well.
Zero in his awakened state (X5) cares nothing about the outside world, not even the Mavericks. He is focused solely on one goal: X. The phrase "new world" means nothing to him. Omega's personality is not Zero's original programming. Inticreates left some ambiguous possibilities of a linkage but confirmed nothing, and even if such a link did exist, Omega would still be a derivative work.
Sigma is certainly thrilled by the idea of awakening Zero's true self, going so far as in X2 to claim Zero was destined to follow him, but can we honestly believe that? When a voice in Zero's head is encouraging him as he's about to hunt down Sigma in X6? Sounds like somebody was being played.
Are we honestly to believe that Zero, and by extension Wily in X-series timeframe, wishes to remold the world when Wily sealed Zero until such time when he could challenge X? When after an allegiance with Sigma to unlock Zero's true potential, leaving the world in shambles as a side-effect, Wily simply drops off the face of the Earth? I don't buy that.
Sometimes the credits make mistakes.
True enough, I recall the Ostro/Birdo mixup. I guess we'll have to leave it at that.
KI: Some people think he might have been inspired by Sagat from Street Fighter because of his look, but that's not actually the case. Sigma and Zero basically represent the idea that nothing is absolute. Sigma was a powerful leader of the Maverick Hunters but after Zero passed the virus to him, his allegiance changed. Circumstances can change anything, and nothing is absolute.
Inafune is merely stating a sequence of events, not a cause and effect (although the implication is there, it's not directly stated). He did fight Zero, the virus was passed to him, and his allegiance did change. That the second caused the third is a logical assumption but still an assumption. As for the X4 book quotes, given that X8 is supposed to be a revelation on a possibility that the Hunters, and the vast majority of the fanbase, left totally ignored, why is it anyone's surprise that older sources don't sync with it?
The virus, regardless of its effects on Sigma's judgment, was key to his role as leader of the rebellion. That he sics Vile on X in MHX on the sole grounds that he can go Maverick of his own accord says that such a phenomenon, while possible, is exceedingly rare. Sigma needed the virus solely for gathering support if nothing else, to say nothing of giving himself near immortality. It definitely affects his abilities, and perhaps it did affect his judgement, but that doesn't mean he can't draw the same conclusions. Philosophy is one thing, implementation is another. If he decides that Reploids would develop ideally without humans, how far is he willing to go to see it happen? Would the virus change that? Would a space development production line churning out new allies change that?
You see how the virus making him evil, ruthless, etc., does not necessarily mean that the virus is responsible for his belief in Reploid superiority.
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