The whole goal of MGS3 is for Big Boss to defeat The Boss.
Big Boss is plenty stronger than Tidus, I think.
http://www.gamefaqs.com/poll/index.html?poll=3802
http://www.gamefaqs.com/poll/index.html?poll=3834
http://www.gamefaqs.com/poll/index.html?poll=3765
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