The Megaman battle networks were my favorite GBA games next to pokemon! (Especially the third and second one). This looks great, I'll play it when I get a chance and give a better analysis of it.
One thing though, Megaman only has...four moves. Obvoiusly we can't get around this (yet) as a community, but just, one of the points of the Megaman battle networks was that there were many chips and such. Maybe make a "move learner machine" and you can customize your moveset at will depending on what "chips" you collect.