>>37483142I'd go for something more subtle, such as imprint all gym leaders some backstory that makes them more human. They don't shove it in your faces like many fangames love to do but they have some kind of schedule where they close their gyms and take some off time.
After you beat them you can find them where they are, earn some respect from them and, as busy people they are, ask you favors. In these favors you can chat explore their struggles, victories, how they are coping, both successfully and not successfully with their past mistakes, and even with loss. If ERSB ratings are no problem, you can even include an addiction overcoming story.
Villain may have a strong nihilism v/s transcendence problem and after you beat him and their team some things just click on him. If you find him in a close city he might invite you to a cafe and tell you how difficult is to amend his previous mistakes once his views on life and death had changed.
Overall I would make a grimdark story but with a positive message, about how to deal with your problems, accept them and use them in your favor.