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I like the original the best because I think it had the best setting/atmosphere, best characters and bosses, and best story overall.

Next I liked MGS 3 because it had the best gameplay out of the three, and it had pretty cool bosses as well, but I think it had the weakest story of the three.

Part two was good, but could have been great if the story was a little less confusing, and you could play as Snake more or if Raiden wasn't so weak.