I say 'Armorless' becase, honestly, Samus' armor is waaay more advanced and powerful than John's. But, without it, she might as well be a near-Spartan.
So who wins in hand--hand combat, no rules, no armor?
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Samus is physically stronger than John. Her suit only was built for her to physically live on Zebes (due to the environment) when her parents were killed. Upgrades only augment the suit's abilities such as weapons. They don't alter her physical abilities at all. John's suit gives him super strength, durability, etc. Outside the armor, John is just a normal human who doesn't do anything extraordinary. Samus wins. Big time.