That makes a difference? My guess is you never played a single Metroid title. Her weapon is mutli-use and has it's own ammo built in per weapon (not shared). By the time MC has his next weapon out she will have vaporized him with one of the many beams she can use, not to mention she can shoot rockets. MC shield, his everything is toast. 

It's not a question of how he will die, it's a question of when. MC is not agile, he's not fast. He's gimped by many factors in this. it doesn't matter if he has an army, she can blast that army away in one shot. It doesn't even matter if he usues covenant weapons. Her technology is far more superior to that. Given there is no restrictions, she must also have access to every weapon she can bring to the table. 

http://metroid.wikia.com/wiki/Power_Beam

But that's unfair because reasons.

Why don't we just make Samus an infant, then MC can finally beat her.

Varia Suit has no AI, its a biological suit that is connected to Samus's nueral network, so I'm not sure what Cortana would do...?

In Metroid: Fusion, after getting attacked by the X-parasite, they had to surgically remove the suit from Samus' body because its a part of her just like her skin.

"Sorry Chief, I can't get in that suit. The technology isn't familiar to me at all. It's like it came from another universe entirely or something."

Also, Fusion Suit.

She has a one hit kill weapons... Cortana would have to take time to hack the suit. Like she took years to open doors and shit. MC has no instant kill weapon. Unless the Knife isn't nerfed.

Samus does not need to be on the planets land, she could be in orbit and fire that energy ball capable of destroying planets.

I wonder just how powerful power bombs are? According to Adam, they can vaporize humans instantly. Funny, they go off right next to Samus all the time and she's no worse for wear. But then again she's not human. Or her power suit can withstand explosions that would incinerate humans without breaking a sweat. Or both.

Either way, it does not bode well for Master Chief, who can be killed by regular human grenades even in his Spartan armor. The kind of grenades that do not instantly vaporize humans.

Power bombs aren't some kind of special, end-game one-hit-kill weapon like the Hyper Beam. They're a regular part of Samus's arsenal. You usually get them around the mid-point of Metroid games.

So, we're done here, right?

Samus, of course, and she is also a much cooler character.

Would be one interesting fight.

I think it would end with MC impregnating Samus with their kid killing both of them.

I wonder if that's even possible, she's not exactly a human.