I really want to like this. It has so much potential, particularly the instruments and mixing.
The first problem is less about the arrangement. The Wily theme from MM1 is just really boring. It's a very standard progression that doesn't go anywhere or introduce a compelling melody, and unfortunately the arrangement doesn't mess with it at all.
Now, connecting it to Napalm Man's theme is a good idea, as that one's all melody, and a good one when arranged well. And the instruments here are perfectly suited for that. Yet . . . we never really get the melody. The first time through, there's just no melody, and the second time, it's a loose interpretation of the melody. The melody is never clearly established at any point.
I think one problem is setting up Napalm Man's theme to be the climax of the piece, rather than the core refrain. Since it's the only melody here, it ought to be more prominent. Wily's theme is a decent B section. Instead, the roles here are reversed.