It's called character development and realism. He was sort of like Myrel from the first MGS, she was scared to kill someone at first. Can you imagine going through hours of virtual reality training thinking you can deal with death, then sent in the middle of a terrorist situation and had to kill someone for the first time? I'm sure Snake was the same way when he first shot someone dead, but like he said,"I've killed enough already to know what death looks like." Well, it was something along those lines with Psycho Mantis tells Snake the one thing they have in common..Point is, Kojima is a great story teller and owns Miyamoto any time of the day