While this comic may have originally been just a joke about Dr. Light's doing a half-assed job at reprogramming Mega Man, in later storylines it took on an interesting twist. Some fans started noticing that Mega Man doesn't act like a complete idiot when he's facing off against Robot Masters, and can actually come up with pretty clever schemes to destroy them. Yet, when he's away from the Robot Masters, he tends to act like an idiot.
This led some readers to believe that perhaps when Robot Masters aren't around, when Mega Man's primary mission is not activated, he falls back to his secondary mission, as dictated by Dr. Light in this comic. But when facing off against Robot Masters, his primary mission kicks in and he quits behaving like an idiot, long enough to defeat his enemies and save the world.
Of course, this was never my intention in the first place. More likely, I was unconsciously having Mega Man acting less like an idiot so that the idiotic actions of the Robot Masters would be funnier. So really, his behavior was really more the result of bad writing than some sort of clever foresight. But hey, who am I to question fortune? Once the fans started commenting on this behavior, I took advantage of the situation and played it up, even making it an important plot point later. Which I suppose is kinda clever.