As I've mentioned before, the first game storyline went fairly quickly from Robot Master to Robot Master, completely skipping the levels in between. If I couldn't come up with any good jokes about the levels, why bother including them? It's a theme I would use in the later parodies... you know, when they still resembled the games.
In the early game storylines, I made an attempt to match Mega Man's attack to the Robot Master's actual in-game weakness, at least the weakness attributed to him by whatever strategy guide I was reading at the time. For example, it was suggested that you use Cut Man's blades against Guts Man, and Guts Man's blocks against Ice Man. I have no idea what strategy guide I was using at the time, since it seems like every strategy guide I can find suggests a completely different order, so I suppose it's entirely possible that I was hallucinating the entire thing.
Anyway, in the interest of keeping the comic interesting, I figured Ice Man would have a trick or two up his sleeve to make Guts Man's attacks ineffective, forcing Mega Man to come up with something a little more clever to defeat him.