The only problem with introducing yet another complication into the storyline is that Mega Man just got back from his last adventure, which pretty much took place immediately after the fight with Bob. I really didn't want to have him start on another storyline just yet, so I figured I'd give it to Proto Man instead. I mean, I couldn't have the comic focus solely on Mega Man, right?
Oh, wait, in the early years of the comic, that's exactly what happened. In fact, there were times I thought about renaming the comic, if only to have the title indicate just how important Mega Man is to it. Unfortunately, by that time, there were already dozens of other Megaman-based sprite comics out there, all with names like "Mega Man Adventures" and "The Megaman Chronicles", and I realized that to change the name to something like that could reduce the comic to just another Megaman-based sprite comic, and it could easily get lost among the rest of the crowd. So I kept the somewhat unusual name, even with the current lack of focus on the Bob and George characters.
And, given how the focus changed in the later years, I think it worked out pretty well.