Tried this myself on 3DS. It's very strange. I played through Charge Man in both versions, and MM5 is very much inferior to RM5. MM5 has frame skips all over the place, and it makes bits of the background blur into a mess every few seconds. I played a little of Star Man's stage too, and the meteors right at the beginning are obviously a lot smoother in RM5. Guess I'll be sticking with Rockman Legacy Collection.
Also, what's up with the weird vertical black line on the left side that happens in 3, 4, 5 and 6?
It's not in 1 or 2.
I haven't played the original NES versions in a very long time, so that could actually be part of the games, but it looks really off. Guess that means I'll turn the borders off.