My personal belief of the optimal control scheme for megaman is as follows.
Shoulder buttons must include Shield,grab, and jump. Personal Buttons used are L for jump, R for shield, z for grab.
Reasons for this is shoulder jump allows all benefits of tap jump without the risk of accidentally jumping EVER(jump cancels, the ability to do perfect retreating fairs/advancing bairs via c sticking the opposite way you are moving), while allowing you to have full sideways momentum the entire jump, also you can keep your thumb on the c stick AND do perfectly buffered aerials, no travel time for your fingers unlike X/Y jump or limits like tap jump.
Shield you always want instantly available in case of a sudden need for shielding or dodging. Grab is so you are able to z drop and keep your thumb on c stick for instant catch or toss options with no finger travel time.
A is attack, B is special, Y is grab and X is jump. You want 4 different inputs for the optimal mashing method.
C stick is set to tilt stick for no air momentum loss aerials, buffering up airs out of jump (both of these ONLY possible with tilt stick, smash stick aerials disallow both). And for easy access to tilts, also gaining the unique ability to nair while moving without dropping momentum via perfect diagonal inputs on the tilt stick(once again, smash stick cannot do this.) smashes meanwhile arent that important for mega so its a win win. You do lose access to the easy super glide toss upwards throw you'd have with smash stick though, but luckily..
You can do both up and forward super glide toss by keeping A+B smash enabled and learning to do the inputs with that. Tap jump is off as it has a chance of accidentally triggering jump and you get ALL the benefits of it and X/Y jumping by using a shoulder button to jump.
There is my control scheme that I consider optimal for mega, any questions or suggestions please do post but I cannot think of any way to improve this control scheme on the GCUBE controller.