I swear, when I started anime/manga you would get the eventual gag of the fat ugly guy who was the trope villain. It was fun, especially how you could always go "Pig die" and so on. But now it's been a few years, and my take on it has started to change. It is like whenever any action series has an element of mystery to it and they start looking at suspects I can just point right away and say "It's him. "he looks old and ugly" "Fat and ugly" just "Creepy and Ugly". Then, of course on the flip side when ever something happens and you want to find a "good guy" in the sub mystery genre they are just as easy to find they always have the "Handsome guy halo". All this stuff is a bit sicking it is so commonplace that before I knew it I had taken it for granted. No matter how you look at it is it not just discrimination in fiction. No joke i hate when people start getting political about the fictional stories but this type of moral attribution to physical attributes we do in real life. I am not taking some great stance to say it should be fixed or anything, don't get me wrong. I'm just griping here, that it "Tough being ugly" in fiction. It seems to automatically equate to evil unless you are a Quasimodo type of character and fucked up as it is they tend to just die so that the main character can swear revenge over the corpse.
Had a similar experience recently with a random youtuber for a random game, where he ended up getting flak just for not being good-looking 'disgusting neckbeard basement dweller' with everyone hopping on the bandwagon 'he looks like a pedo' and everything else. Anonymity really brings out the ugly in people, no pun.
A good mystery genre would not evaluate appearance unless that appearance becomes a key factor or a plot point. It's completely possible to write an entire mystery novel without actually describing someone's level of attractiveness.
No I'm not talking about mystery stories but mainstream action one's that stumble across a "Conspiracy"
Tbf, appearance does play a role on how much we like/dislike a character. Like, it's pretty rare for someone to dislike a character's design, but still enjoy the character themselves. So... It kind of makes sense for the authors to lean on that aspect and make the characters with the most appealing designs the ones you like the most, while the most dislikeable ones being the ones with the least appealing designs. I do understand your point, but if I was the director of an anime, I would definitely make sure all the main characters are attractive and would probably make the villains less attractive... The exception being when I wanted to specifically play with the fact that a part of the main cast was ugly, like... They could have issues with their appearance or something. Otherwise I'd totally stick to the appearance tropes... It just makes more sense in trying to appeal to your audience.
It is a distasteful fact for when it is concerning fiction but admitted or not how we view reality is in our fiction and when people see these stereotypes played out in the stories they love even if they are not conscious completely of it they will accept it as a form of verification that this form of behavior is correct. It is the same way people might be off-put by a "shady" person in real life and be cautious of harm.
While I have seen some stories that buck the trend, usually as the story's selling point/point of differentiation, this isn't just limited to fiction, as Titan LLS is pointing out just above. People regularly get away with things that others wouldn't due to being physically attractive. It happens regardless of gender, but Girls regularly take advantage of this. I've heard stories of an ex-girlfriend beating her ex's face to the point where he had to hold down one of her arms to stop her from hitting him in the face, before he went to the police to report the assault. He got laughed at by the police, while her fraudulent claim that he choked her got him a year of jail time. Attractive people just get more leeway than unattractive people do. To the point where story writers make pretty characters because they want them in their stories, while the unattractive characters are either background characters or treated harshly. Hell, regularly when this isn't the case, the "unattractive" people are only overweight, and showcases that they can become attractive if they simply lost weight. Chōji from Naruto is an example of this, as are several "reincarnated into an ugly character from X game" stories. Chōji was only overweight due to his Chakra Techniques needing him to be, and was posited as being quite handsome for the short while when he was thin (and that's ignoring the entire "Sakura can't hold Sasuke responsible for anything because he's too pretty" trend), while I know of several Reincarnated Into An Otome Game Stories where the MC reincarnated into a "Fat Pig" Villainess, only to have all the capture targets prostrate for her due to the replacement MC being thin. I would not be surprised if the only major difference between the original character and the replacement MC was that the replacement MC was thin, the boys of the story would still flock to the thin MC due to them being pretty, and thus any actions they take are excusable.