Beauty equals good, ugly bad
By conventional beauty standards, that is.
It has been done to death. It’s lazy and boring
I know, I know, originality doesn’t exist anymore, but that doesn’t mean you should automatically default to what came before. I guess it’s a clichè at this point.
Visual shorthands are useful because they can convey a lot of information without actually spending that much time explaining them to the audience, plus they like figuring things out for themselves.
It goes back to the old chestnut of showing and not telling, but there are certain dangers involved:
As I wrote here, putting thought into why you are giving someone certain visual traits can save you from having unwanted implications.
Your story will be less predictable
Audiences are so used to this dichotomy, that it often gives away who the antagonist is way before they should know about it. By designing all your characters in a way that’s less common, you might be able to surprise your readers.
You are hurting people who aren’t conventionally pretty
Having variety of appearance is important, and by portraying the bad guys as the ugliest bastards on the planet, while having impossibly attractive good guys… yeah. You see where I am going with this? You can dodge this by having diversity on both sides.
Seeing yourself in fiction as a positive force is huge, and not being demonized for a change is even better.