Analyze the superhero and determine the events causing them conflict within the story. Design the super-villain to embody those conflicts. Give them the ability to cause relevant, believable problems for the hero and to harbor directly contrasting objectives.
Write a full character biography for the super-villain. The biography should include a life history from parents and childhood to the moment before the story starts. Detail their inner conflicts and give them authentic, conceivable reasons for wanting to foil the superhero or achieve conflicting goals.
Rewrite the story where the events no longer match the personality crafted for the super-villain. Ensure every action that the super-villain takes is in pursuit of the goals detailed in the character biography.
Have someone else read the super-villain's character biography to provide feedback and highlight any potential cliches in the character's personality, powers, abilities or objectives. Remove and rewrite anything flagged as a cliche.
Rewrite the story to introduce the super-villain early on, and to establish their objectives. This should take place before the hero and villain meet.