I want to stick up for Nathan Drake a little bit. I had this conversation with a friend a couple of months ago when he said the same thing.
Yes, Drake does kill a hell of a lot of people, but he only really does it in self defense, most of the time the people he is killing are hired thugs who have been given the simple instruction, stop Drake. So put in this position, what choice does he have, does he let these people kill him first? That would make for a very short game.
In both Uncharted 2 and 3 there areas where people are not shooting at him and they get away without being murdered.
And ok yeah, I can understand your annoyance with him not showing any remorse for killing the people he does kill, but you can explain this away by saying that its just typical action hero bullshit. Does James Bond or John McClane ever show any remorse for blowing away the small army thats trying to kill them? No, its usually a clever one liner and then sex with the girl. I don't see why Nathan Drake gets flack for doing the same thing.
Now, him being the destroyer of lost ancient artifacts I can't defend...