I'm not enjoying walls of text, so I'll try and be brief, difficult as that may be (EDITS: So much for that). Also, "who we are" in spite of memories/goals is a philosophical debate, so I'm not touching that.
Regardless of whether Serges ordered him to align with Sigma or Zero chose to do so of his own will, in that X2 scenario they were partners. It demonstrates loyalty extension or transference is possible for an awakened Zero state.
It's self-serving as long as Sigma's going to bring him to X.
We also have to question what state exactly Zero is in, considering how it contrasts to X5, and although I know you'll argue against me on this (we've been over it before), I still perceive a power difference between the X4 flashback and MHX, which leaves X2 as the only aberration. Zero uses identical moves in X2 whether fighting him or not.
Regardless of X4, it's rather clear that the X2 "awakening" is not the same as the X5 Awakening. And we could really use more details as to why that is, but as far as I know, there is only speculation.
That Wily was developing Zero to help him conquer the world is self-stated fact in Power Fighters.
I don't deny that. But Power Fighters is concept, and concept is not programming. You make the presupposition that it is, and that's the problem that I have with your statement. Your explanation doesn't address that point. To establish that world domination goals exist in Zero's programming, a statement must be made at or following his completion. We have no such statement. Power Fighters is only to be expected, it's in-character for Wily at that time. But if he wanted the world, he could have had it, all he had to do was unleash Zero before X was ready. Why wait? Why challenge X to open combat when your ultimate weapon being his best friend presents much simpler and more expedient methods? Why back off when the world is in shambles after X5? Wily is considerably less aggressive than we have known him to be in Classic-series, and I have a hard time believing that he's working towards the same ends that he was previously.
Omega is likened to Original Zero's program and character, not actually "Awakened Zero." Technically the code talked about in Power Fighters is the earliest known "original" Original Zero program, and anything later added to be primarily about X could have been patched in later
Yet another loophole to add to the ambiguity of the interview, and one more reason why asking the fans to "use their imaginations" is not a concrete answer as it invokes a wide variety of ends depending on who you ask. If we're differentiating between Zero's initial concept and Zero's finalized "Awakened" programming, that's opening up a whole new can of worms.
I'm seeing Sigma Virus vocabulary all over again.
The Zero we see in the X4 cutscene is about as original Zero as we've witnessed actively, but is his behavior indicative of Wily's plan for the original Zero? He appears to attack anyone who approaches, He behaves wildly, energetically brutal, focus-less. Hundred year sleeps tend to cloud one's memories in many cases, has that happened here?
We can only speculate, but I tend to lean towards Zero in some manner not being fully optimized, lacking his X2 revisions, and quite possibly lacking Wily's command itself (if such is necessary and not just encouragement/gloating ala X6). Hell, it could have been intentional for the sake of preparation, since both Zero and X suffer a lack of experience in X1 timeframe. They're formidable, sure, but a long way from the force that they can become.
After the double KO, they resurface.The Original Zero ideal would probably not have included standing up and protecting X, declaring hatred for Sigma and denouncing his own evil.
That happens every time, including X4 in which the hunter persona to our knowledge never previously surfaced (albeit we do not know the details of what went on in the repair center, but given Zero sharing the same mysterious design nature as X, I have a hard time accepting that it was anything too radical, such as the "Cain-programmed" speculation of many fans). The X5 scenario doesn't stand out from any other in that fashion.
If Weil or his associates did remove the goodness, the virtuous Hunter Zero elements from the equation, recreating many key elements to the Original Zero program, the personality closeness may in that way be greater than Awakened Zero's.
From a storytelling standpoint I don't buy that as being a viable explanation. If so then Weil outdid Wily's plans. Besides being improbable for another evil-doer to outperform Wily with his own creation, I also find the power scale to favor AZ over Omega. AZ has the Genmurei, Shin Messenko, Shin Getsurin. Omega lacks such enhancements, your own attack translations actually confirming his use of the inferior Messenko. He does, however, posses an extra few centuries of experience, doubtless contributing to his variety (case in point: Rekkoha).
Which reminds me, Awakened Zero as we see him in X5 is still incomplete. Can't ignore that, either, although I do wonder if the use of Genmurei isn't supposed to mark the completion of his transformation, as victory is impossible at that point.
Wily's massive failures. In X2 Serges tried to restore the program with virus, but if that is thwarted he just whips out a copy instead. Neither were successful ventures. X5 involved a similar plan to dissolve Zero's Hunter sympathies away in light of his true self thanks to the concocted Zero virus, and per one scenario it did for a while, but ultimately failed. If Isoc had managed to finish whatever he intended with Zero before X6's events, he wouldn't need to capture him.
I'll grant that it's possible, but I find it unlikely as it strikes me as entirely too convenient. Especially X5 which is presenting us a worst-case scenario. The mere existence of the hunter persona is in itself an oddity, are we to honestly believe Zero is left as a blank slate without the virus?
Part of this ties in with my belief that Wily was not consistently interested in world domination over the course of Zero's construction. But there is another thing. Many MegaMan series emphasize the power of the heart, and it's on those grounds which Bass, Zero's predecessor, is most frequently criticized. Zero's heart may well be necessary as part of his power, Wily finding a way to harness/bend it rather than ignore/overwrite it. There is also the possibility of a last-ditch effort for survival as well, the idea that Zero turning nice when he's beaten may be intentional to ensure that X never destroys him.
Ultimately the above paragraph is entirely speculation. But you can see, there are a lot of different ways it can play out.
Also, about X2's copy, Serges knows the control chip is one-of-a-kind. That was probably a move to appease Sigma more than anything else, I sincerely doubt he honestly expected the copy to stand a chance.
X has already fielded the question. A noble hearted Zero is stronger than an evil one because his power is used for the right reasons. Parallel to why Forte can't win in classic. Not a question of technology but of soul. The kind of thing that tends to drive villainous number-crunchers crazy.
Something we both agree on. However, as I said above, I consider it probable that Wily caught on to that, which would explain oddities in Zero's personality, both why it emerged in the first place and why it was never eliminated by his creator. Domination puts Zero on the wrong side of the fence, but a rivalry, as is Wily's self-stated focus in X4, does not lend itself to either good or evil. And an honorable rivalry can be a great source of power, hence Zero challenging X openly (EXE manga touches on this same concept with Bass Cross MegaMan). But only to one's self, not to the rest of the world. The rest of the world has to stay out of the equation, hence AZ's disregard for the Mavericks, for everything, that is not X. He wishes neither to see it preserved or destroyed, it simply doesn't matter.
That's how I see it, anyway.
Now, to nip a counter-point in the bud, yes, X talks about sensing evil within Zero, I'm aware of that. Would X consider apathy to the extent necessary in AZ to be evil? Probably. But more likely, I think X is sensing the virus and exercising his pre-conceived notions of it (not at all unreasonable, given what the virus does to anyone who is not X, Zero, or Copy Chip equipped). He likens it to Sigma, but to an even greater extent than Sigma himself. If this were connected with personality and not to the virus, it ought to reassure him against Lumine's ramblings in X8. Such is not the case. Moreover, X even specifically likens his senses to what Zero taught him of things that cannot be analyzed correctly, that is, the Sigma Virus.
So, no path is without resistance. We simply have a difference of opinion in what constitutes the least resistance.
Since the charged outputs are changed in MHX it puts less emphasis on shared technology than on similar looks.
Not entirely. They preserved the fact that the Z-Buster allows X to charge special weapons. That's technology that Zero doesn't utilize, and although chargeable special weapons are something of a standard in buster upgrades, forgoing it is not unheard of (X5, Falcon Armor). So the fact that MHX didn't raises an eyebrow.
For them to have never identified Zero's original code or its role grinds against the nature of what they accomplished there.
That assumes the good Zero and original code were separated from each other in the first place, which is in and of itself a speculative point. In the absence of the Sigma Virus and its derivatives, sans Mother Elf who is unable to influence Zero (if anything circumstantial evidence suggests the other way around), that's extremely difficult if not impossible to confirm.
Area X-2's backgrounds hint at a pretty clear undersanding of Zero's body, who made him, and why.
The point at which that data was obtained and the clarity it offers is unknown, not to mention the Omega symbol is featured prominently on those displays. Although going out on a limb, one could even speculate that the descriptions and information on display may not have even come from within Zero, merely Weil's using his (Zero's) registry number to refer to him. If Neo Arcadia was sitting on the full knowledge of Zero's true history, I don't think Phantom would be finding any grand revelations in Cyberspace. He and the rest of the Guardians, especially after Copy X (MK1)'s defeat, should know the full story.
Making any observation about reasoning behind events in a "storytelling context" is entirely arbitrary, unless you're going by the intentions of the story writers. Said story writers insinuate a link between Omega and Original Zero's programming. In that light Zero's question may not be as important as Weil's response.
Of course it's hypothetical, half our posts are. I simply see that as Zero asking what's likely on the player's mind, and Weil's response conflicts with his own actions from the game's introductions. He was already gloating with implications that Zero shares no relation to his "original" self, something which X later rebuts. Weil's mindgames do not allow his dialogue at that point to be taken at face value.
Said story writers explicitly stated that Weil programmed Omega at least in part. Again, they merely refused to make the statement that he did it without aid from Zero's previous programming. No matter how concrete you take that it still means Weil had a hand and isn't just appeasing the god of destruction, contrary to what his response indicates.
Most of the Isoc stuff is a difference of opinion in villainous policies, there is little backing to act-versus-think beyond personal opinion at this point. I will say, however, that there is a difference between hesitation and calculation.
If Serges hadn't seen some value in Sigma, he didn't need to build Sigma a new body at all. As leader of the Counter Hunters, he was acting head of the second wave, and he himself resurrected Zero's body. Simply claiming to pick up in Sigma's name could have been enough to unite the remnants of his forces under himself. He could have spearheaded everything. He had a choice not to help Sigma, or sabotage him in his revival.
You can read that two different ways, though. As an underling (which is what he is under Gate, don't kid yourself), or a partner, he removes himself from the equation and does not make a lasting stand in any instance. As leader of the Counter Hunters, him making no move to seize power on his own can be taken to speak against world domination and more towards alterior motives, as we have never known Wily to carry any intention of sharing his throne. The fact that he plays along with somebody can very reasonably be taken to mean that he DOESN'T want what they want, since when does Wily spread the wealth?
If Wily is interested in the aspirations of the likes of Gate and Sigma, will he not betray them eventually if they are no longer needed? If so then the fact that we didn't observe such a betrayal in unsuccessful scenarios is moot. World domination only leaves room for one at the top. But Gate and Sigma have alterior motives to simply ruling. Sigma, to exterminate humanity for the future of Reploids. Gate, to achieve recognition for his work and vengeance for crimes against him. How long do you think Wily would fly with that?