You’re designing a villain, and you know what devious, evil things they’re going to do, but you need to give them an appearance to match their despicable soul. Whether it’s their clothes, their hair, or their devilish horns, we have a tendency to don them in black. Black and darkness is a sign of evil, right?
It makes sense that humans are afraid of the dark. It’s a primitive survival instinct. We fear the dark, because we don’t know what’s in it. Sure, there could be something good hiding there, but it’s more likely to be something like a predator. So after all these years, we’ve learned to fear the dark and associate the color black with evil, the unknown, and scariness. But since we know where this fear comes from, should we continue to use it?
Why this is bad: If you’re looking for the element of surprise, coating your character in black is certainly not a way to do it, especially if they’re also snarky, witty, or mischievous. Black hair or wardrobe is a giant, blinking, light-up sign that says, “BAD GUY!!!” When you make your reveal later that “the guy who’s been dressed all in black and speaks in riddles is the one who killed Shane!”, nobody is going to be surprised. The villain uses shadow monsters to do his dirty work? No one is surprised.
Some authors try to circumvent this by showing the villain in all white, especially when the villain thinks that they’re actually good. The author might even do this just to be ironic, as is the case with Lilith from Supernatural. Still, we’re not surprised when this person turns out to be evil. All suspense is taken away, not to mention the age old rule of “light defeats dark.” The hero wears white or gold, the villain wears black or red. We know. We get it.
There is also some racial ickiness to go along with it. Historians used to use this common fear of the dark as a way to condemn black people and claim there was some “moral right” to enslaving those of dark skin. After the death of the founder, the Church of Latter-day Saints claimed that black people were cursed with the Mark of Cain and were no longer allowed priesthood (this idea has not been formally renounced by the church, but is no longer enforced as to my knowledge).
Does this mean you’re racist if you make your villains dress in black or control the dark? Of course not! But I think it’s something to be aware of.
How you can fix it: Unless they’re an overdramatic type, don’t let your villain wear all black ever. Also, it’s probably a good idea to avoid black hair. Make your villain dress within the bounds of their interests and personalities, and don’t force them into something just because it fits their archetype. Outside of the world of appearance, maybe think about giving them an unexpected power, one that doesn’t fall into stereotypical evil or good. Magneto is a good example. While it can easily be argued that he’s not evil, he is still the Big Bad in most X-Men universes. His powers over metal aren’t particularly evil or good. They’re just powers.
Bottom Line: Finding out the chick who has been dressed in black this whole time is the villain isn’t going to surprise anybody. Find ways to subvert stereotypes without necessarily flipping them by treating your villain like an individual.