Honestly, I think the way everyone is playing Mega Man isn't playing into his greatest strength. You say MM has problems with all these match ups (fast, bulky, reflectors,ect). I say MM is my character who has a pretty fair match up against any type.
The trick is simple. Aggressive lemons. Lemons lemons lemons. With lemon shots, and MM's good movement you can always apply some decent pressure.
F-tilt Lemons are great for movement, but on hit they don't apply enough hit stun to keep you safe during the three shot cool down.
Standing lemons are safe.
Short hop lemons to fade away or approach.
And the hard body hit of the standing or air lemon.
Knowing when do move between those 4 lemon types allows MM to have fairly great control and keeps him safe from reflectors and speed monsters. It's kind of hard to explain but I hope to have some video soon.
Ah, that's definitely something I'm not doing. Need to practice my lemoning, I guess. Do they do enough damage and knockback to control the stage enough, though?