The idea of a Snake the War Hero using his super-soldier skills to try to expose illegal arms dealing, and the way the game encourages but does not require non-lethal play, really helps. Like, you can just go nuts and kill tons of people, but the game always makes it clear that you don't half to, and that the in-game vision of an ideal soldier is someone who accomplishes their goals without killing anyone. It makes the player a moral actor within the illusion of choice offered by a video game. Yeah, you can kill that guy, but you can also knock him out or just sneak around him. In later games you can even brainwash/recruit him at which point, simply by changing his uniform, he goes from "Bad guy" to "Good guy".

Putting mercenaries front and center also supports this notion that most soldiers, most of the time, are just hapless mooks being used by some Great Man to further their agenda, and the nationality and ideology of the average soldier is just an accident of birth - Big Boss isn't on the side of any ideology, he's on the side of the soldiers, and he wants to create his weird fucked up state where soldiers fight for themselves (Because he's a deeply unsocialized super-soldier who has literally no skills except those pertaining to war and can't imagine a life where he is not a soldier).

Of course in real life most mercenaries are deeply ideological, often far more so than regular troops, but for the purposes of the game it says a lot about how the dehumanization of the enemy is a tactic of the oppressor, and how war is an ultimately futile pursuit where powerless people kill each other for no gain.