I'd like to say Deus Ex: Human Revolution.Non-RPG
Red Dead Redemption.
Spec Ops: The Line?
Back when it came out I was fairly impressed with Spec Ops: The Line, but later I noticed that the game was praised for doing stuff that MGS1 and 2 did more than a decade ago and it got shit for doing so.
For non-RPG. . . *shrug*
Everything that comes to mind would be "mature" in the generic ratings way; blood and tits.
The Metal Gear Solids touch on some mature themes. . . but they're also hard to take seriously.
The games know how to have fun with their own universe, that doesn't diminishes the mature themes the series touches upon.