Eggman and Wily are easily two of the most iconic villain geniuses of all time. Nobody can forget their giant robots or their powerful schemes of world domination. I would argue that Wily’s intellect definitely surpasses Eggman’s though. He helped to build Mega Man, which exceeds Dr. Eggman’s inventions. (The ones that he manages to hold on to anyway) Eggman’s Egg Emperor is a powerful threat though and I don’t believe that Wily’s machines would really be able to stop it. It’s just too large and it could fire powerful lasers to take Wily down for good. Eggman wins.