You have a hero. He/she is awesome. Your beta readers love him/her.
You have a villain. Unfortunately, your beta readers find him/her murky and hard to believe, so they don’t really understand your story. What is their problem?
The problem is not with the beta readers – you haven’t gotten a grip on that villain yourself, and therefore the antagonist has no motivation for being evil other than possessing a bastardly disposition, which doesn’t make a really compelling story.
First you need to understand what defines evil: Google Definitions defines evil as:
e·vil
ˈēvəl
adjective
- profoundly immoral and malevolent.
“his evil deeds”
synonyms: wicked, bad, wrong, immoral, sinful, foul, vile, dishonorable, corrupt, iniquitous, depraved, reprobate, villainous, nefarious, vicious, malicious; malevolent, sinister,demonic, devilish, diabolical, fiendish, dark; monstrous
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The villain in a story can outshine the hero to an unfortunate extent.
I remember a popular B movie from the eighties called the Highlander, where the hero was played by Christopher Lambert. The plot involved a group of immortal beings doomed to duke it out with each other through the centuries until there would be only one left. While the Lambert character was heroic, sensitive and endearing, the villain was so powerful, so much fun and so badass, he took over the whole script. I’ll never remember the actor who played the part or even the name of the character. I remember all of his scenes, though. Terrific!