I don't think Dr. Wily was expecting them to acquiesce so quickly. I'd bet this has something to do with an episode of Star Trek: Deep Space Nine, in an episode called "Our Man Bashir", where, long story short, a holodeck villain is confused when the secret agent hero agrees with his plans for world domination/destruction. It's a good scene, one well worth ripping off.
One of the reasons I chose to show Dr. Wily in his Skull Head... uh.. vehicle-thingy is that there are too damn few sprites of Dr. Wily, especially of the 16-bit variety. In this case, I wasn't confident enough in my spriting abilities to do anything more than adjust the storyline to allow for him to be attacking from his vehicle there. Later on, I would attempt to create some half-way decent sprites, and then Deccus would completely negate my efforts by making his own, superior sprites, which I would turn around and later use myself, in both the comic and in the Cataclysm movies.
You know, I'm not sure why Wily's disintegration cannon is so small. It seems like Wily would be the type of megalomaniacal villain that would built huge weaponry for no good reason.