It's really an elegant plan, sort of. If Mega Man really has been successful solely thanks to his dumb luck, then removing the stupidity block, a block Dr. Wily put there in the first place, should remove that good fortune, causing Mega Man to fail. However, once the stupidity is removed, wouldn't that make Mega Man an even more dangerous foe, by making him competent?
Nonetheless, Bass has a very good point here. Wouldn't it just be easier to just destroy Mega Man now, while Dr. Wily has the chance? By destroying the Mega Man of the past, history would change and maybe Dr. Wily would've been successful in one of his bids for world domination. Of course, if that happened, then how could the events in the comic possibly come to pass, and how would Dr. Wily have the chance to destroy this Mega Man in the first place? It's definitely a messy time-traveling paradox.
Of course, the same thing could be said of Dr. Wily's plan, so what difference does it make?