Why does it matter to you if you have a braindead macho marine or a Nathan Drake in your game about shooting? If Uncharted's multiplayer, with its interchangeable "Heroes" and "Villains" factions, is anything to judge Naughty Dog's views by, they don't think that there's any appreciable difference if the game is only about shooting (as UC2's multiplayer is).
As you state here, developers have a vision of how they want their game to turn out. Uncharted isn't about shooting, it's about being Nathan Drake, a friendly, rough-and-tumble explorer who knows his way around both a gun and an abandoned ruin. Both the story and the gameplay are essential to establishing that experience, and getting the player excited and engaged in the tale these characters create through their actions.
The best way to convey this experience may not be through perfectly balanced and enjoyable gameplay, though. In Ico, your character frequently combats shadow warriors with little more than a stick, and the combat mechanics consist of little more than mashing Square. Theoretically, they could be more involved, and your character more capable. They are not, because Ico is a game about being a motivated youngster attempting to escape a castle with a girl, not a game about being good at hitting things with a stick. In this way, the gameplay is "compromised" to better suit the tone and the character. This is one example, but many more exist.
Naughty Dog feels that the best way for Nathan Drake to interact with the environment is to shoot many, many enemy mercenaries. That is their decision as developers. That said, there is no reason in particular why it would be impossible for Nathan Drake to go about things in a different way in the game. That way might even be less "fun" from a gameplay standpoint, but it might better fit the tone created by the setting and character.
Certainly, this stance is nitpicky as hell, because it's essentially criticizing the creators for not using their premise to make the game you felt they should make. But if this disconnect between character and gameplay in Uncharted were solely imagined by an individual, it wouldn't keep coming up in different places. Creating a plausible and consistent world is a process that involves both story/characterization and gameplay, and sometimes, it can be more important than either individually.