Big Boss > all. Therefore MGS3 has the best characters. It also has the Boss and the Sorrow. And Little Baby Ocelot (I <3 Josh Keaton). Volgin is pretty badass too. EVA ain't bad. And THE END. Best boss fight ever.
And MGS2 has Rose. UGHDFAUDLFK.
Gameplay: 3 > 2 > 4 > 1
Characters: 3 > 1 > 4 > 2
Story: 3 > 1 > 2 > 4
3 is clearly the best.
I should also mention that I love Raiden and I love MGS2. But aasdifugha Rose is so terrible and Cambell isn't that great either. Vamp is kinda cool in 2 but he's terrible in 4. Fortune is stupid. Fatman is the worst aside from Rose. Solidus is cool at least. Him, Raiden, Snake, and Otacon are really all that MGS2 has.
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~Halo Now darkness takes you... forever.