Let's see:
KOS-MOS is a powerful opponent able to takes of damage and has lots weaponry (beam cannons, wristblades, a handgun, etc.) plus has the agility and strength to deal with tough opponents. No doubt the strongest protagonist in the game (besides chaos with his full power and Jr. in Red Dragon mode).
Megaman is not as agile as KOS-MOS but has great strength (since he was able to hold the ceiling of a collapsing base for a bit) and he has robot master powers which include:
-Protoman's shield (which can block many projectiles)
-Super Arm (allows Mega to throw large boulders with one hand)
-Elec Beam (powerful electric wave)
-Time Stopper (stops time in the area for a bit)
-Crash Bomber (sticks on surfaces and then explodes)
-Atomic Fire (a more powerful version of the Mega Buster)
-Gemini Laser (laser that ricochets around the room)
-Hard Knuckle (rocket punch strong enough to bust walls)
-Spark Shock (powerful electric ball)
-Shadow Blade (a huge shuriken)
-Gravity Hold (sends enemies upward and damages them)
-POwer Stone (three rocks circle Megaman and act as a barrier).
-Knight Crush (shoots out a spikeball on a chain)
-Danger Wrap (traps enemy in a bubble with a mine)
-Slash Claw (picture the R-Blade but invisible)
-Noise Crush (shoots out damaging soundwaves)
-Tornado Hold (throws a fan that can trap enemy in a tornado)
-Astro Crush (causes a rain of meteors)
-Flame Sword (take a guess)
-Thunder Claw (it's just Bionic Commando's grappling arm)
-Homing Sniper (locks on target and shoots a missile)
-Dive Missile (homing missile)
-Rain Flush (creates acid rain)
-Tornado Blow (blows away enemies and projectiles)
-Black Hole Bomb (creates a black hole)
Megaman can also call in his robot dog, Rush who can be used a springboard or as an aircraft. He can also combine with Rush to give him air-capabilities or to give him extra strength. Megaman cannot survive a dip in lava though.
Despite all of Mega's weaponry, I have to give this fight to KOS-MOS. She was able to absorb an entire alien fleet and blocked a phase transer cannon which is capable of effacing a star. Let's not forget how much damage she's capable of doing. When she was just an archetype, she killed a group of armed soldiers using nothing but her own body and was capable of causing an explosion of wide radius. In an alternate timeline, her power struggle with an U-DO wave caused the destruction to the surrounding planets in the area. She once cracked a window that was made to withstand asteroid impacts using her fist.