As inspired by nick's "10 things you didn't know about sk" I wouldn't mind the idea of "sneaking past" explored for some levels - maybe a stratum where you use stealth module?
If you could tie rewards to NOT killing (or delaying the killing) of the monsters - (sneak points, treasure that exists only when the monsters are alive, hopefully others can come up with some other ideas), you'll get that behavior.
That and I wouldn't mind a level or two with some "secret" doors. A castle should always have some "hidden passages". :D
Rewards like a bandanna with an infinity symbol on it that gives you infinite ammo.
And if you beat the stratum the third time you get a tuxedo instead of the sneaking su- I mean armour.
And take Maryl's ending. Otacon lives in that one, where Maryl dies in Otacon's. Just survive Ocelot's torture events. BUT DON'T USE AUTO-FIRE, BECAUSE HE'LL KNOW.