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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That depends... Zero Mission zero suit Samus or SSB: Brawl zero suit Samus? If it's brawl, then Chief is screwed. EDIT: You also forget that Samus is no pushover outside of her armor, she trained as a child, is very athletic, and had her DNA modified in order to wear a power suit. [Edited on 06.02.2012 7:45 PM PDT]