Not saying the Megaman plot can't be ADAPTED into something better. Anything can, really. The Protomen is an example of that.
The best story that could ever be made would be if Megaman Universe was some kind of ultimate multiversal multidimensional crossover between all different Megamen, together to stop a threat from annihilating all of reality.
(I really gotta put some damn variety into my recent literature. This [parasitic bomb]'s affecting me badly >_>)