The following post is written assuming that you meant actual incredibly bad 'set pichus on fire' villian.
I think the main reason is that a true villain, not just a character who is a rebel or who does the odd bad thing, is very hard to write because it's difficult to empathise with them. As a writer, if you find it hard to explain to yourself how the guy justifies giving a room full of pichu the ol' gasoline and lit match then you're never going to be able to explain it to your readers and the character comes off as 'a jerk for the sake of being a jerk'.
Even if the writer can empathise enough with the hero to write the fic, there's the problem that the viewer might not. A story starring someone who is doing unforgivably bad things runs a few risks, especially when it's a fanfic. People will assume things like "This is a hatefic", "This is a troll" or "This person's just trying to be cool and dark" even if it's brilliantly written. And that's if they get past "Man, this guy's a jerk. I don't want to read this".
A hero going bad is a different matter, since they have the reader's (and the writer's) empathy still from the beginning of the story. People can forgive a lot if you're the main character and they liked you at first. But here you run the risk of going too far and getting accusations of character derailment. You'd have to make the transition believable.
'It's difficult and risky.' is the short answer to your question. But if it's something you've been planning, you should go for it.