I'd say that if Naked Snake didn't know by far the most important aspect of his mission, then he's basically clueless. You can't go "He knew everything except that the mentor he was agonizing over was actually a good guy and he was being lied to the entire time by everyone and killed her for almost no reason". Raiden knew his mission too, and it never changed throughout the entire game.
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Black Turtle did a pretty good job.