As everything hints at Wily existing inside of Repliroid bodies that share his likeness; why would it make use of such complicated reality altering?
I think, that he used the virus to escape Cyberspace. I do not know, if he was a cyberelf-like being in the beginning or the virus gave him a body to interact with the material plane.
If he "escaped Cyberspace", he'd be a substantiated program like the Light hologram in X5, he wouldn't be occupying robotic bodies.
Wily died, but using the virus he became somewhat of a ghost; his soul could exist without a body and is now occupying the bodies of Repliroids made in his likeness.
Don't quote me on that - I'm posting this for the sake of marshmallow man sighting this and then seeing whether this is fact or not - but I thought I read somewhere the Nightmare sort of did the same thing. It would be possible since it's derived from the Sigma Virus and the Earth was still scorched with it.
The Nightmare Virus is so powerful it gives itself a solid body. Sigma Virus does this only in high concentration or by using external power. This process is 'substantiation' of the Virus.
Substantiation of other cyberspace programs (making them escape cyberspace) is also possible. But only the ZERO Virus has caused that phenomenon. Though the Gospel Server's radiation did the same, that's a different series. The Nightmare does do something similar, but it's not the same as what the ZERO virus does; I would liken it a lot more to how a Cyber Elf seems to change the environment.
The Sigma Virus being the basis for all these viruses would have similar properties.. it's just not powerful enough..
When did this interview happen? I had no idea Wily was brought back by the virus.
Remember when Inafune debunked the cataclysm? Same interview.
http://www.capcom-unity.com/s-kill/blog/2008/09/05/inafunesan_answers_your_questions
1) Did Zero really "kill" the family between the events of the Classic Mega Man and X series?
KI: No, Zero did not kill them. According to the way I created him, Zero is not such a person--it is not in his profile.
4) What was the inspiration for Sigma?
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.
6) What happened to Dr. Wily in Rockman X series? Are Dr. Wily and Dr. Weil the same person? Were they ever supposed to be?
KI: A large amount of time has passed between the classic series and Mega Man X. Dr. Wily had died in the interim but was brought back by the virus. Dr. Wily and Weil are not the same person. It is ironic though, because Dr. Wily created Zero, and Dr. Weil used Zero, but ultimately it was a copy of Zero's original body with a different mind that defeated him.