How Dr. Wily's Posthumous Influence Lived On in the Megaman X Series
Although I refuse to believe that Serges and Isoc are Dr. Wily but at least, they could have been results of Dr. Wily's influence, Dr. Wily has a posthumous influence that even after he died of old age, his influence lived on in the next century. So I was thinking the answer lies in one person- Zero! Zero was his final creation and successor. It was revealed in Megaman Zero that he wasn't able to use Zero immediately because of that bug but had him tested further. Dr. Wily knew he wasn't going to last long either so he probably wrote his last will and testament to Zero, inserted his life's work into Zero and maybe it resulted to Zero's programming flaw. Dr. Wily had years of knowledge and trying to let Zero understand them in one sitting may have caused it.
For Zero, he was also the carrier of the Evil Energy, which may have evolved into the Maverick Virus containing Dr. Wily's influence in it as he also had Dr. Wily's knowledge in his head, heck Zero may even have a copy of his own blueprints allowing Serges to know of it later. Even if Dr. Wily had died, Zero would be a carrier of that influence.
For the Serges/Wily connection, it is possible that Serges was a robot with some of Dr. Wily's memories. Remember even if Dr. Wily had died, his legacy lived on. Considering Serges was the leader of the X-Hunters, it's possible that he went Maverick having at least some of Wily's memories. So how did Serges, Violen and Agile have the blueprints of Zero? It's possible that while Wily had long died, Serges was an attempt to spread his influence. Maybe Dr. Wily created the X-Hunters centuries ago and were made to serve Zero. Another possible theory is that whoever made Serges had Dr. Wily in mind. Remember Dr. Wily has a legacy so it's possible that the late doctor's plans got downloaded somewhere. Serges while not being Dr. Wily (literally) was a robot based on Dr. Wily. Serges piloted his own machine into battle rather than confront Megaman X without a vehicle. The Japanese dialogue has him saying he's defeated by a memento of Dr. Light. Again, if he's not Wily, at least he would have had some of Wily's memories. Dr. Wily always had a backup plan which ended up creating Serges in the next century.
In Megaman X4, it was revealed that Sigma, like Wily, was a traitorous scum but a real sicko compared to the former big bad. Sigma fought with Zero and during that time, Sigma punched Zero's crystal which may have caused the virus to infect Sigma. Although what is possible is that, Sigma went Maverick at will, gave in voluntarily to the posthumous influence of Dr. Wily and became a more sinister version of Dr. Wily. Zero who was supposed to carry Dr. Wily's ambition and succeed his creator, ended up becoming a Maverick Hunter while Sigma carried Dr. Wily's will instead. Sigma encouraged some of Dr. Cain's robots to rebel, led the rebellion just as Dr. Wily reprogrammed Dr. Light's first six robots to be his robots.
For Sigma, after having the Maverick Virus in his system which evolved into the more lethal Sigma Virus for Megaman X5, carried on Dr. Wily's will meant for Zero. Sigma used the new knowledge he had downloaded for Zero. He may have even found out of the existence of Serges, Violen and Agile whose origins are ambiguous but may have been prepared by Dr. Wily years ago to assist Zero should he awaken. Sigma also had some more of Dr. Wily's influence when he manipulated Dr. Doppler into creating him a super body (his hardest form to defeat in ALL Megaman games) and two, when in Megaman X5, he managed to turn himself into Gamma Sigma. If Sigma was able to learn about Zero's past through the data in Zero, it may also explain why a Gray Devil was in Megaman X5 or how he even learned of Dr. Wily's hatred for Megaman. Again, Dr. Wily is nowhere around but his influence lived on like how late scientists' inventions are still being used today.
Megaman X6 also hints of Dr. Wily's influence in Isoc. Although Isoc is NEVER confirmed to be Dr. Wily but it's highly possible he was designed after Dr. Wily which the same can be true for Serges. While Dr. Wily is not the type to be willing to take a lower position, Isoc was willing to be Gate's assistant. Just me thinking... Isoc may have had known of Dr. Wily's works, started to study them and eventually learned of Zero. It was possible that he had Dr. Wily's influence in him even if Dr. Wily was long gone.