But here's the thing, at the end of the day, despite the absurdity that MGS regularly plays with, it's still asking questions. Just like Sci-Fi heavy hitters from Blade-Runner to Deus Ex, it still asks you to think and answer questions about its world, its technology, its people, and how all of that applies to *our* world. Even after Raiden flips a Mecha and chops someone into actually 300 unique slices, the game is still willing to stop and ask you with a totally straight face "Are you a moral person? Can one be moral in any armed conflict?"
"Sci-Fi" like Star Wars or 40K or Destiny very rarely stops to ask you heavy questions, just serve up a new fantastical plot so you can go revel in a fiction, not expect you to pause and do any soul-searching. To me, that distinction matters far more then if all the technology or antics in a given fiction are legitimately plausible.