I think it was around this time that Proto Man's personality really started solidifying in my mind. Once I'd realized that Mega Man was to be the comic relief, I knew I needed a straight man to play off of him, someone for the audience to relate to, and ultra-cool Proto Man fit the bill.
In addition to being the straight man, I also knew Proto Man would be the "older brother" figure (and not just because he is Mega Man's older brother). That is, sometimes he's embarrassed by his little brother, but Mega Man is still family, and Proto Man will stick by him and take care of him. Of course, that doesn't mean Proto Man won't sometimes have a little fun at Mega Man's expense. I mean, they're brothers; that's what brothers do.
Proto Man's line in the second panel was originally supposed to be referring to the idea that since the Author was supposed to be posing as Mega Man earlier, he couldn't tell the difference between them. I suppose, looking back, it could also just as easily be a joke about recolors, but since the stigma against recolors was years away, that viewpoint can only be appreciated in hindsight.