While perhaps too much of a sitcom cliché, I always do enjoy the "right behind me" gag. And while most of the time it happens to Dr. Wily, we see here that it does happen to other members of the cast on occasion. Though, it would probably have been funnier had Mega Man actually said something nasty about Bob, aside from just calling him a jerk.
I mean, to really make the joke work, I think you have to have the character go on and on, ranting about the person standing behind him. In fact, I think the longer the rant goes on, the better. Hell, I'd even take it to the extreme, having Mega Man continue ranting long after Bob has made his presence known, standing in front of Mega Man, waving his hands, trying to get his attention. That'd be funny.
Of course, one problem with that is that Mega Man doesn't know anything about Bob yet, so he really doesn't have anything to bitch about. All he knows is what George just told him, and that isn't much. Maybe later on, after they've all gotten to know Bob better, this joke could be done properly. But right now it seems more like a joke I threw in because the opportunity presented itself, not because it was the right joke at the time. Which is probably exactly what happened.