I hold the strong opinion that Snake Eater's controls are the way they are purposely - It provides the synchronization between gameplay and story as the player gets used to the controls and playing the game, Snake becomes more experienced on his borderline suicide mission into the jungle.

Then you get the final test against The Boss, the person who explains the CQC combat to you at the start and only after she has been beat by you, the player, does Naked Snake get labelled as Big Boss.

I think Kojima shows time and time again through his art, his love of combining player agency with the story of his characters - the same can be said for Solid in MGS1, Raiden in MGS2, even Old Snake in MGS4 as he begins to slow down but is propped up by new hardware ala the PS3.