The moral, here, was unmistakable, of course. Rather, it's the way Kojima went about conveying it that was so interesting. Instead of using the story and dialogue sequences to communicate to the player, MGS3 managed to use the elements of player choice to set the medium of a videogame apart from, say, books and movies. In a sense, Kojima gave you a portion of the game entirely, and somewhat perversely, player-created - that is, a product of nothing more than the player's earlier choices - and derived a meaningful message from it. He completely surrendered his game to the whims of the player's choice (which stands as artistic anathema to people like Roger Ebert), and in doing so, he got across exactly the message he wanted. Indeed, it is the player's personal involvement in the game - and thus killing dozens of virtual human beings - that makes this scene so compelling. Books and movies, as passive media, relate a message to the reader by presenting a story where the reader sees the consequences of the protagonist's decisions and interprets from there. Videogames, as MGS3 would have us understand, can be aimed directly at the player.
It is the regrettable truth that as popular as the Metal Gear Solid franchise is, it's never popular for any of these reasons. If MGS is the original TACTICAL ESPIONAGE ACTION game and MGS2 is the one with the annoying protagonist, MGS3 will be forever remembered as the one that is half James Bond, half John Rambo. But underneath that action-movie exterior lies a brilliant sense of game design that does, ironically, what so many games fail to do adequately: tell a story only a videogame can tell.
Pat Miller has been doing this for way too long.