Unless BOTH Snake and Samus's matches against Zelda were comlete flukes, I just don't see how Samus is winning after all this. I mean Snake beats Mega Man and Sonic, (Who beat Crono, who was is Samus's tier before this) Samus did poorly against Tifa and Zelda.....and now she's winning?

I suppose the answer is that Samus stayed consistently strong, Zelda and Tifa boosted for whatever reason, Sonic Crono and Mega Man all fell a little bit in varying amounts, and Snake boosted but not to Samus's strength.
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While the first two matchups were deceptively disappointing, I should have known the third time would have been the charm for Solid Snake! Unfortunately for me, Karma Hunter did.