There's no doubt Dr. Albert Wily is probably still an iconic villain in Capcom even if he's nowhere near awesome as Sigma is. So he belonged to the lighter and softer Megaman series that was the first in line (Megaman 1-10) to where his role was this- he was once a friend of Dr. Light but later, he turned against his own friend for his own crazy world domination schemes. In Tokustasu, you might remember God Neros from Metalder or Doctor Man from Bioman. So what's up with him? Dr. Wily is pretty cruel but also hilarious, which he usually has half-brained schemes for world domination that was until later.
In Megaman 4 and onwards, one can see the Megaman series was taking a darker direction. Dr. Wily in Megaman 4 kidnapped Calinka, Dr. Cossack's daughter so he could force Dr. Cossack to give him the new technology to defeat Megaman and regroup his robotic empire. In Megaman 5, he frames the traitor Protoman in the form of the Darkman robot. In Megaman 6, he actually goes as far as to disguise himself as Mr. X to actually start a contest where he reprogrammed various robots to help him. It was in Megaman 6 we thought we saw the last of him but the game popularity caused him to return for Megaman 7. I think Megaman 6 was supposed to end the franchise.
In Megaman 7, Dr. Wily manages to escape prison with a backup plan but hasn't changed his mecha design. I mean, that Wily Saucer was getting redundant. Meanwhile he creates his first evil Megaman in Bass... which however developed a set of emotions to go against him.
So Bass and Treble were created to counter Megaman and Rush in the seventh game but later developed some kind of different goals. Bass only wants to beat Megaman not caring about world domination or calls Dr. Wily as "half-brained". Unlike Megaman, Bass' buster is focused on a rapid shot of very powerful bullets and this leads me to theorize that he could have actually been remodeled into Axl in-between either by Wily or somebody else for the X series since both display a cocky attitude, a certain degree of dislike for Megaman and a fierce independent spirit.
So Dr. Wily did have other plans. In Megaman 8, he harnessed some evil energy that may have become the Maverick virus in the future. Dr. Wily's plans for world domination went serious this time and in Megaman and Bass, he created King to replace Bass. In the download only Megaman 9, he framed Dr. Light and in Megaman 10, he unleashed the Roboenza.
Now Dr. Wily later felt that Bass was no longer fit to be successor and he created Zero as his new "son" to succeed him in the case of his death. However he wasn't able to fully use Zero much less train him because Zero's cruelty before he became good, exceeded that of everyone. But he probably sealed Zero realizing Megaman was upgraded into Megaman X to continue his work in the case of his death. So probably he decided that in the right time, Zero would awaken and his "son" would continue his work. So he did make some "hints" in the Megaman X series. Zero appeared as a faster, more agile character with his mastery of swords plus Zero's saber is probably the most powerful sword in the series.
References to Dr. Wily were made in the X series. In Megaman X2, one can see Serges a robot who looks like Dr. Wily. So probably in the span of 100 years, Dr. Wily did convert himself into a machine so he would live on beyond his human years but no official word of Dr. Wily being Serges or even Isoc (in Megaman X6) was given. I think Wily is Serges seeing he knows too much about Zero and two, he later rebuilt himself into Isoc but either way, he had lost his glory as Sigma was just too powerful compared to him or it's just possible that Isoc and Serges are both Dr. Wily clones containing his memory that even if the scientist had died, they continued his job. Dr. Wily was revealed later to be Zero's creator in Megaman X4 (play Zero's story mode and watch the beginning) and in X5, some references were made to him. In X5, the third stage in the fortress battle has Dr. Wily's logo made or even in the first stage, the Bio Devil reappears and has the W logo. In the final battle of X and Sigma, Sigma makes a reference to Dr. Wily as "having created some robots and you two know each other" to which suggests that Dr. Wily could still be alive as a non-combat reploid and gave Sigma that power. In X6, Isoc could as well be him (thus making Serges also Isoc) but was later destroyed. perhaps ending his downplayed menace once and for all.