Damn right, that was Wily's Zero.

Ciel (or whoever, I don't pay attention to MMZ) "fixed" Zero, though, and made him less...I dunno, psychotic.

X series Zero has both sides, the maverick/nightmare/etc and the "normal" Zero.

Still unsure what made Zero "half normal", though. Obviously in the X4 scenes, Zero was maverick/nightmare when he fought Sigs. But seemingly afterwards he's fine? God knows what happened there.

And the "official" (I use the word loosely) explanation is that they went ahead and installed a Suffering Circuit copy on Zero afterwards, which viralized his "violence program" and turned him into a carrier.

I prefer the virus transfer opinion.

Supposedly Zero was "fixed" when he had his robosoul transferred to the copy body, since the entire point of his cryosleep was apparently to get rid of the virus.

(OK, the script doesn't actually say that. But in his X6 ending which Capcom said takes place after all the other X games, Zero goes to have something fixed, entrusting X to protect the world.)

So I wouldn't be surprised if Omega was at least created by modifying whatever dark side Zero left behind in that body. Either way, I agree that Omega essentially represents a "what could have been" sort of outcome.