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The Twin Snakes was directed by Quentin Tarantino fan Ryutei Kitamura. Explains the limb-chopping. Kojima was only the Producer. He didn't waste his time with TTS (which was in my opinion a piece of garbage remake that didn't have any real bonuses or different gameplay styles), cause at the time he was working on MGS3.
That's right, Naked Snake and Raiden > Solid Snake.
My REAL opinion: Naked Snake > Solid Snake > Raiden.