It all depends on where they are fighting. You have give them a setting. Master chief would win if he had ready access to weapons, cause Gannon is a relativly slow character, although I'm not sure how well the chief would do considering he can't dodge roll like Link, which helps to escape his magic balls of doom. But considering he has basically infinite life, he can just have time to let his shield recharge inbetween attacks, I think he would be ok.
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