I think they take the "its a game" thing way to far. The patriots are the game developers. the game itself is the simulation not the events in the game. Big Boss is named Big Boss because that is what you call the boss at the end of the game and why in the games after liquid and solidus said they were the next big boss. Every game someone tells snake he can't leave the battle field until he dies because he will be the protagonist until they kill off his character (or his voice actor dies). I bet they think they are very cryptic and no one gets it.
Something was missing from MGS3. in every MG game (except the first one) a character that "died" in the previous game came back. In MG2 it was big boss. MGS grey fox. MGS2 liquid. since MGS3 takes place in the past, no one can come back.