El Cazador de la Bruja
Half of one episode in and I'm already having flashbacks. The dull realism of the animation, the flat look of the backgrounds, the languid direction, the gunslinger female protagonist that's a bit older, the emotionless girl with a powerful secret that's a bit younger, the smirking antagonist who's evil for evil's sake, the secretive organizations that control things from behind the scenes, and secret plot to control the world. Yes, this is the same guy and the company that produced Noir and Madlax.