More stories would benefit from having repeating antagonists who are kind of bastards, but not monsters. Characters who can mess up the protagonists' day sometimes, but also be okay to work with in others. It gives stories a way to have serious problems that take a lot of their skills that aren't fundamentally escalatory.
Firefly was great at this, because of the "on the fringe" nature of the situation. Mal gets shot (at) multiple times by Patience, but he is still willing to work with her on occasion.
This works really well with morally grey protagonists, but can also work with good ones as well. Have someone who has a different Lawful orientation who disapproves of methods, or wants more credit, or whatever.
If the protagonists are grey, this character cannot be "bastard who has a heart of gold" because that ruins the whole thing. They have to be the type of person who acknowledges being outplayed and only takes it slightly personally.
