Sadly for Mario this is a fight he simply doesn't stack up well against his opponent. Allow me to run through the Doc approved list of powerups.
The feather allows Mario to fly, destroy enemies with a spin attack and also provides some protection as well as it can be used to reflect projectiles. However, ice missiles kind of screw that up, as they'll explode on contact rather tha be reflected and move faster than Mario in the air. leaving Mario encaced in a block of ice and prone for a finishing blow, however he uses it. Additionally a screw attack would punch straight through the cape and to the chewy plumber centre it was protecting.
Samus can walk through lava with the Gravity suit. Fireballs aren't doing shit. She's also got a flamethrower and plasma beam just as a "anything you can do I can do better"are included a la Super Smash Bros.
Much like the feather, this one allows him to take flight, but in a far more controlable fashion, but provides no defensive enhancements. Samus, who's faced many different types of flying enemies from swarmbots to space dragons would have no problems shooting down Mario.
As the name suggests, it turns him into an invincible metal man for a period of one minute. Samus, no stranger to fighting forms she cannot hurt would figure out that she needs to dodge until the time limit expires, aided by Ice projectiles, Metal Mario's speed reduction and her morph ball, it would be no challenge to her to wait it out until he's mortal once again.
This turns him invisible and gives him the ability to walk through some walls. However, Samus has been dealing with enemies who can turn invisible for quite some time. With her Thermal or X-Ray visor she will be able to see where he is and just keep on shooting until it wears off or Mario dies.
Turns him giant and indestructable. Samus would once again have to keep dodging, and with her superior agility she could.
This one gives Mario extra ability to stop the shit out of things and also gives him some degree of protection but is lost if Mario takes a hit. Samus is used to aboiding enemies which try to crush her, with the added danger of shockwaves that also do damage (that the shoe doesn't produce). It's a good powerup, but not one useful against Samus.
Causes Mario to swell up and float slowly. Of all the powerups Mario's got, this one is the least helpful. All it does for him is make him a big slow moving target, exactly what you don't want to be when you're fighting an experienced bounty hunter armed with lethal weapons.
We all know what the starman does, Samus may not but she knows enough about fighting to never allow her opponent to touch her. Once Mario stops sparkling she can finish him off with extreme prejudice.
I like Mario and I've played quite a few of his games, but this isn't a fight he can win.
Samus goes to the finals.