Go back and in and make your villain or antagonist a better character (not a better person, necessarily — but possibly?) Think about the Shakespearean notion of foils, and ask whether your villain and you protagonist have things in common or things that they do exactly opposite from one another. Could you write two scenes, one about the protagonist and one about the (or an) antagonist that parallel each other? What about the antagonist’s origin story? It may not figure largely in the project, but give that villain a childhood, a coming of age, and a formative trauma that made them into what they are. Also, when seeking ways to deepen simple or flat secondary characters, consider widening your point of view (just for research purposes) enough to ask whether your character’s antagonist is someone else’s hero?