I've been working on this story progressively for years. The problem is that I made the villain when I was super inexperienced, and he now falls short as a character. He's the stereotypical "I eat puppies and nothing about me is human" villain. I know the way to give him depth is to add a genuine motivation and give him more humane traits, but I'm having trouble.
For context:
The plot of the story is that the villain, known as James Rugsworth, creates a lab so that he can experiment and essentially create superheroes. James employs friends from his youth by force (they are not allowed to leave, usually he fakes their deaths for them). James has a twin brother, Jason, who works in the lab and is one of the positive forces of the story.
A couple things to add, James is the father of the main protagonist, Swift. Jason and James grew up with good parents. They don't have a tragic backstory.
I have no idea why James would be bad but Jason would be good. Again, they have supportive parents (mostly). James currently is a wife beater, completely inhumane and has very backwards beliefs.
How do I make my villain… human?
I had the same problem, but really you just need to go back to their beginnings to see what would make them tick. Looking back on my own villain I had nothing that would make him power hungry or selfish. Instead my villain became more of a fallen hero looking for a second chance, the influence of another making the way in which he gets that second chance far more dangerous to my protagonists.
What would make James immoral? Did he have a mindset that would make him think his parents were favoring his twin? Did he have friends who had parents that fought and then accidentally made problems in his own family seem bigger than they were while Jason had better influences? Was there any teasing or jokes he could have taken as bullying? It also sounds like you can make a situation where James thinks he's doing the right thing, as most villains think they are in the right. Does he ever go into or have a friend affected by bad law enforcement or the law in general? Were superheroes, such as from comics and shows, a big part of his childhood? Perhaps he thinks trying to create superheroes is right no matter those affected, that he'll save more people than he's hurt when he succeeds. Finding that could also find a weakness or soft spot, something that makes him human.
(First off James Rugsworth is a really cool name) IOnlyHave1Project has great ideas, the only one I might add is have you considered making him…not a villain? what I mean is, it's a kind of universal truth that nobody really believes that they are evil and I think you have a really easy way to do that here and make James the hero in his own mind as most villains often are. Creating superheroes is on the surface at least kinda a good thing even though the way he's doing it is horrible. You could make him a well intended extremest or a firm believer that ends justify the means or the needs of the many out way the needs of the few - essentially the end goal is worthy so it doesn't matter how many people have to suffer for a worthy sacrifice. The wife beating could have a lot of reasons and I guess I'd need to know more about them both to give a good explanation but examples of reasons he could justify abusing her might be things like: He's trying to 'make her stronger', He's afraid she'll leave him so he's using fear to keep her in her place, He believes theirs some greater evil out there and keeping her with him by any means necessary is the best way to keep her safe. etc.
Another way you can justify the difference between two people with the same back story ending up on opposites sides of morality is…. well mental Illness is thing… And those it does run in families it can skip generations or affect one sibling and not the other etc, Mixing in a little ASPD could help explain biologically why his mind is twisted.
Villains are hard. I, too, have a character that was made in a lab and the person who created her I made "evil." However, he's not a typical villain. He created life because all the life on his planet was wiped out. That's just his motivation though. Everyone has their own. I don't want to give you a villain so I'll give you some tips to work with. The biggest one I have is to flip the story. To through it from James' point of view. Does it makes sense? If it does, you're golden. Genuine malice is rare so why does he do what he do? However, malice does work sometimes, usually when the villain is corrupted. Hope this helped! Spend lots of time on your villain, they take time. Good luck!