They could have definitely continued improving the Mega Man idea through the various gaming eras For instance, why did they never make a Mega Man First Person Shooter game? The game is literally running and shooting, it would have just been a different view.
It would have been awesome to see Mega Man take a development style similar to that of Metroid. They could have kept the 2D style going on portables and 3D, plus Hi-Def 2D, on consoles.
Why Capcom never did that, I have no clue.