I'm here to rep Gunslinger Girl. The original light novel is 14 or 15 chapters and the anime adapts only the first 4. A Hitman 2016 style game where you could get in, assassinate your targets and get out like in Hitman cleanly would be a sick gameplay loop to base a game on. There should also be combat missions too, because that's part of the story (they raid several safe houses in the anime, one being in the first episode).
Currently (Re-)Playing: Starcraft 2: Legacy of the Void Multiplayer, The Legend of Zelda: A Link to the Past
Currently Watching: The Shield, Stein's;Gate, Narcos