What you're having trouble with is reading too much into a vaguely worded non-canon piece of text that was never even shown within the same series!
I find it ironic that it's only "non-canon" when it suits your current point. I don't recall you having any qualms about using it as a proof when it came to X being the only Reploid to lack bias. Which, by the way, is
another thing not covered in the games. It's badly written and confuses the story, (and if it's non canon then it absolutely has confused fans) so why the Hell shouldn't it count? We're talking about Capcom's poor writing here.
Everything up to X5 is pretty easy to understand, in terms of viruses. After that tho, the virus situation becomes something of a mess. There's too many. And they mix up the terms. A sign of poor writing and lack of foresight.
Frankly, their treatment of "viruses" is another sign of bad writing. Oh, I understand it just fine. But it's cumbersome and has the elegance of an elephant. The "colony virus" is a great example of this. Somehow, crashing a space colony spreads a virus about. And the purpose of this new virus is to interact with a known virus and, somehow, merge to create a close approximation of Zero's original virus. All this as opposed to, say, Wily just releasing the Zero virus. In terms of the story, the colony virus never needed to exist in order to get the point across.
Occam's razor: X5 would have been better understood if it didn't exist.
The Sigma virus is the Maverick virus. One of these terms doesn't need to exist. Since Zero infected Sigma it's only logical that the term "Sigma virus" doen't need to exist.
I actually tried explaining X5 and the Zero virus to my sister, who knows nothing about X, and she was thorough confused and didn't care for it. Lord knows I've seen newbies come in various forums asking about the virus. Even the Megaman Wiki can admit it's confusing. It didn't start out that way, but it sure has become much more confusing that it had a right to be. And that's mostly because of the amount of viruses within the series along with the unnecessary "suffering circuit" explanation.
Suffering Circuit = Worrying = The ability to think, feel and make your own decisions = free will.
No way that the Sigma Virus which creates irregulars relates to free will, that's just such a ludicrously overcomplicated concept!
Oh yeah, a virus that overrides free will relates directly to a concept introduced first in a
source book released
only in Japan is soooooo accessible to fans. Yeah, why did I ever think it wasn't accessible to people who play the games? I mean, X1 is all about suffering circuits. It's "suffering circuit" this and "suffering circuit" that. Why, even Dr. Light's hologram talks about X's "suffering circuit".
Oh wait,
he doesn't! Maybe
that's why it's poor writing!
You have very long posts, but while I have demonstrated several areas where the X series lacks (save for people with the utmost of faith in Capcom and full knowledge of sourcebooks as well as encyclopedic knowledge of all characters and concepts that come from said books and every game) you have yet to provide
any examples of
good writing to balance things out.
So, where is it, Zan? Where's the good writing in the X series? It can't be with the Wily subplot; they switched gears on that after a long buildup with no payoff. Is it with X's story? Because the games focus mostly on Zero and
his story. So maybe it's that? I'll admit that Zero's story is pretty good, despite the series being
"Megaman X" and all. So if the story isn't about the title character, then is that "good writing?"
Is the "good writing" the deep philosophical argument in what happens when you give robots free will? Oh wait, the "Sigma / Maverick / Zero / Nightmare / Colony" virus doesn't make that too much of a choice! Not much of a discussion.
So where's the good writing? Can it be found in X6? Maybe I should ask "Zello?" Is it X7 and 8, where they switch gears completely from the past 6 games to go off on a totally different storyline? And where the title character isn't even accessible at first? Is that "good writing"?
Is it X1's intro; the explanation of who the main character is? "X i the first robot able to think, feel and make decisions"? That
one line in
the first game has caused countless debates / arguments and confusion for years! Surely, you can't think that
that's good writing!
So, where is it? The first three games of the series? 3 / 8, is
that the score? Because that's 38%.
A failure. Is it in the sourcebooks? Because I can't even read them and neither can you. Is it in the information they convey? Information related through
books when the medium is a
video game? Do factoids that can't be read directly constitute "good writing?"
And let's not continue to confuse "done purposefully" with "good". You can do something on purpose and have it fail miserably. It can be done "on purpose" and still be a mistake. Being confusing and ambiguous for the sake of being confusing and ambiguous is not good writing. In fact, it's poor writing trying to be mediocre writing.
You can explain how everything makes sense 'till you're blue in the face, but that doesn't mean it's actually
written well. I didn't say the series was "unexplainable". I said it was written (and implied it was concieved of) poorly.
So where is the good writing?