#1 Space Pirates vs. Covenant: Covenant. A few scarabs could easily kill ridley.
#2 Dark Samus vs. Gravemind: Gravemind. A giant, tentacled being, or a wimpy little he-she? You be the judge.
#3 Rundas vs. Sgt. Johnson: As much as I hate to say it, Rundas. He was one of the coolest bounty hunters, and it's a shame he died. But Johnson is just oldschool. This one's pretty unmatched.
#4 Metroids vs. Flood: This is a hard one. I'm gonna say a tie. The flood have guns and could just shoot the metroids, but the metroids could latch onto their faces.
#5 Samus vs. Master Chief: You speculated that Samus had gotten all her powerups and weapons. If she had all those, yes, she would win, but if she just started out and lost all her stuff, master chief, because he is super skilled and could take Samus out with a sniper, and his super strength is a huge bonus. He'd kick her morph ball like a soccer ball.
~U_K~