So, I personally feel like this is a pretty close match -- like people have been saying, a battle of power vs. stamina. There were just a few points I wanted to touch on though:
1. Does Screw Attack make Samus invulnerable to absolutely everything? I seem to recall playing Super Metroid and having some certain attacks still be damaging -- things like a boss slamming into you. I ask because as long as it's not perfect protection, I think Laser Trident would still be able to cause damage, being a weapon whose entire purpose is to bypass defenses.
2. While I would agree that an entire ship crashing into Mega Man would classify as an OHKO, is Samus really willing to demolish her main mode of transportation -- as well as a reliable source for resupplying -- in that way? And besides, even if she did choose to do so, I'm pretty sure Mega Man would be able to stop time for long enough to at least get out of its direct path, though without proper cover I imagine he'd still be taking some damage from the impact. (And of course if vehicles are allowed, then he'd have Rush Jet, Wire, etc -- as others have mentioned.)
3. How resistant is Samus to being sucked into a black hole? Mega Man has the Black Hole Bomb in this scenario, and I honestly have no real gauge as to whether or not I could expect Samus' armor to protect her from that. I would note that enemies who were usually indestructible could be killed with that weapon in the game that it was used.