Now, try to spot the one that's supposed to be ugly.*
The tiger on the lower right?
In animation, consistent symmetry invariably means a character will usually lean towards the state of being generically attractive. This is a hard rule in Bishoujo Series where even plain characters will look attractive, but fundamentally a result of drawing a character that is aesthetically pleasing. Also, for obvious reasons, drawing a character consistently means the hard and fast details should be easily reproducible... and marketable.
This makes it especially jarring when we're tolda character is physically unattractive, gained a few pounds, or has bad skin. It's too much work to draw these minor details. The only way to combat Generic Cuteness is with a Gonk or you end up with a disarming cutesy look in some wildly inappropriate things.
For obvious reasons this should be weighed against how pretty the general mood of a series is but even your gritty action hero plot will usually reserve its uglies for bad characters — and then they will likely be actual grotesques.
Occasionally this pops up because your story is filled with Loads and Loads of Characters but there are Only Six Faces. Some artists attempt to avert Generic Cuteness by hinting at some form of sorting algorithm of in-universe prettiness among their six faces so that the audience can tell that someone is supposed to be attractive without the characters explicitly stating it, though this may result in making every ugly, plain or beautiful character look even more alike.
One common trick is what distinguishes the Meganekko from the dope with Nerd Glasses. It's not that glasses are ugly, it's just obscuring the face is one of the most jarring things to do, and thus not cute.
This trope can lead to Informed Deformity or Ugly Cute. Contrast Informed Attractiveness. See also Hollywood Homely and Artistic Age. Artist might attempt to dispel this by using a Beady Eyed Loser.
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Anime and Manga
Many male leads in Shōnen are supposed to be average-looking as well but most don't look any worse than any other male character that is supposed to be good looking (barring the local Bishōnen).
Ataru in Urusei Yatsura is frequently described by girls as "ugly looking", even though he's a fairly typical design for a Rumiko Takahashi character. The only thing that really sticks out are his buck teeth and the frequent stupid look on his face.
There's actually a bit of a shout out to this when Kurama tries to time travel so he can see her father (Yet another of her early quests to "Make him good enough to have a one night stand with"). When she starts talking about his face and expression, Ataru briefly imitates it perfectly, then goes into spasm's because "He never uses those muscles"
Yomi in Azumanga Daioh worries about being overweight and thus constantly on a diet, though aside from Tomo's deliberate teasing there's the suggestion this is simply a common teenage obsession.
Miki in Marmalade Boy is described as "cute but not pretty" by Suzu and Yuu says that her face is "ugly", yet she has the same facial design as the other characters.
Subverted with Chisame, in that she claims she's frumpy with bad skin. However, no one else comments on it, and some say she actually is as pretty as she seems to look.
Yotsuba, whose gimmick is being a cook, is a slight aversion, as she is visibly plump but not grotesquely so. And even then, her plumpness is eventually visibly phased out.
Asuna is revealed as an example of this whenever she dresses up, which causes people to remark that she looks stunning when she takes care of her appearance.
Subverted/Lampshaded in Yamato Nadeshiko Shichihenge as the boys of the series want to see Sunako's face, which she doesn't want to show because she thinks she's ugly. After a long chase they manage to pin back her fringe and look at her face, which is quite attractive. Then it turns out they were deceived by a ton of flour that had fallen on her and made her skin seem clear. When the flour is cleaned away the spots and unwanted hair are visible. From here on, however, Sunako is never shown with spots (as a matter of fact, she is often just chibi). Despite being called ugly, the way she is drawn in her full form is no different from, say, the super-popular Noi-chan.
Lina from Slayers is constantly teased for being flat-chested, but she's decently developed for a 15-year-old; Recent redesigns to fix this ironically mean Lina has actually become less endowed as she has aged.
Fuuka from Yotsuba&! is often mocked for being plain-looking, having funny eyebrows, or somewhat overweight (particularly over having "fat thighs"). She could only really be considered as such in comparison to her much more conventionally attractive sister Asagi. Ironically, mangaka Kiyohiko Azuma admits Fuuka really is supposed to have these traits but says they're supposed to be charming.
This is basically what doomed Hideaki Anno's plans for Rei Ayanami. He had intended her to be in the Uncanny Valley... but this trope kicked in, making her look more waifish than disturbing. It's hard to blame the viewers for Completely Missing the Point when the point is shrouded in cute-looking fog.
Naturally, her counterpart Kaworu avoids this much better because of the show's mainly male fanbase, who usually ignore his good looks and see him as a textbook Unsettling White-Haired Pretty Boy. Unfortunately, the Yaoi Fangirl contingent latched onto him and declared him a Draco in Leather Pants. Thus the "Evil Kaworu" manga retool.
Similar to Yomi, Hiro in Hidamari Sketch worries about her weight and her diet, but any differences in her weight aren't really visible to the viewers. Except for maybe that one bath scene in x365.
This can also produce the opposite effect: characters who are supposed to be exceptional are, well, not that much cuter than all their classmates. Haruhi Suzumiya, for example, is considered stunningly attractive, but so is everyone else in the school.
It should be noted, however, that really all of the main and supporting females are supposed to be outstandingly attractive: Mikuru, Tsuruya and Asakura are all explicitly mentioned to be this and even Nagato gets an A- from Taniguchi, as well as occasional positive comments on her looks from Kyon. The trope still applies, however, because minor characters (like the ENOZ girls) look just as attractive as these.
This can be applied to most productions by Kyoto Animation. Another good example is Midori from Tamako Market, who is said to be really attractive, even if every other female character is just as cute
The same counts for Ami in Toradora who, being a model, is supposed to be way more attractive than her classmates, but generally only seems to excel in bust size—barely.
Also for Ran from Detective Conan. Sonoko complains that she pales in comparison to Ran, who is apparently being hit on by every guy that crosses their way- although BOTH of them look just like every other girl their age in this series.
Nadie from El Cazador de la Bruja is supposed to not be that attractive, judging by the responses of some male characters when she tries to act cute—for example when she disguises as a taco delivery girl. Still, her character-design is actually rather pretty, which is especially evident in merchandise for the show. Then again, she does have a tendency to make very silly faces. (Her name is also Spanish for "nobody".)
Ichigo in Bleach - it is frequently said that the best that could be said about his face is it looks 'interesting,' yet he isn't noticeably less attractive than any of the other male characters.
Miaka from Fushigi Yuugi is supposed to be average-looking (kinda the girl version of the typical male lead in a harem anime), but she is far from plain-looking.
Katsura Yukiji from Hayate the Combat Butler is described as unable to get a date and also as she used to be cute. The personality is probably part of it, at least, but you couldn't tell she was 'ugly' to look at her. Or that she was much older than her students... Considering the series, it's possibly intentional.
Even the villains seem to be affected, aside from looking a little darker, there's really nothing to tell them apart from the friendly characters.
Shiruku from Kyouran Kazoku Nikki is supposed to be horribly scarred behind her mask, but once it comes off she only appears to have a discoloration around one eye, which isn't too distracting from her otherwise cute face.
While Himeko from Kannazuki no Miko has several characters lusting over her, she's portrayed as not really being above average in the eyes of most. The other girls are surprised to see her hanging out with the likes of ever-so-popular and beautiful people like Chikane and Soma.
An entire episode of Genesis of Aquarion is premised on the three main female pilots going on crash diets after gaining what normal people would consider a trivial amount of weight. Since they're maladjusted teenage mecha pilots, it's plausible — except that their character animations exhibit no evidence whatsoever of said weight gain.
Nina Einstein from Code Geass is frequently pressured by Milly to lose her glasses, but...doesn't really need to. Nina's plainer and less endowed than all the other schoolgirls in the main cast, but in a show where character design was done by CLAMP, all this means is that Nina is realistically beautiful while everyone else is impossibly beautiful. Including some nearly all of the guys. Girls the world over wish they looked as good in a dress as Lelouch.
Hitomi of Escaflowne has rather plain looks, which once or twice troubles her. She doesn't have a less attractive face compared to other female characters though. However, the series is also heavily populated by pretty Bishōnen.
Sakura of Naruto. She's canonically not that attractive, merely cute-looking with a prominent forehead, but you wouldn't know that to look at her. According to Word Of God, she really wasn't attractive at the beginning. Kishomoto's assistants even reacted at her reference sketch saying "She is not cute". Praise Art Evolution here.
Usagi of Sailor Moon. Especially jarring in that the series uses Only Six Faces. This also holds true for her weight, even though when you look at her it's hard to tell that she's supposedly a little overweight.
Yukinari of Girls Bravo is frequently bullied by girls and is said to be average-looking, dorky, and good-for-nothing. He's also frequently beat up by other girls via a punch/foot to the face for being an Accidental Pervert. However, he has the same facial design as the female characters making him a dude that looks like a lady.
The premise of the manga Family Complex (A spinoff of Princess Princess) is that the main character, Akira, feels inadequate due to being the sole average-looking member of a supermodel-hot family. This may have come off as a bit more believable if Akira◊ wasn't himself a doe-eyed bishonen.
Although not an example of being cute, in Fist of the Blue Sky manga characters that are considered "good" are all portrayed as handsome and beautiful whereas those considered "bad" are disturbingly intimidating at best and comically ugly at worst; Zhāng Tài-Yán is perhaps the best example- the viewers know it's the same person with the same visual features, but he still managed to look significantly different before and after renouncing his evil ways.
Ranma ½: Ranma constantly calls Akane flat-chested. She's got the real-life equivalent of at least C's, same as almost every other Anime girl unless it's deliberate and/or a plot point.
Puella Magi Madoka Magica: Madoka notices that Homura is charming (etc), but since everyone including the males have Ume Aoki's signature wideface, the audience can't see how Homura is supposed to be significantly more attractive than others.
Inverted and defied in The Sandman series, where Despair of the Endless is the exact physical opposite of any woman in the comic books industry.
Aside from a passing resemblance to Amanda Waller.
Serious literary variation: in Tanith Lee's novel The Birthgrave the heroine (who wakes with amnesia at the start of the story) believes she is ugly and spends most of the book wearing a mask because men shied away from her the first time they saw her. In fact of course they shied away because they were astonished by her incredible beauty. But you guessed that already, right?
Elizabeth Bennet could be considered this because Jane is always proclaimed to be the beautiful sister. She is also described as having "more than one failure of perfect symmetry in her form," but her fine eyes and light figure make her beautiful in Mr. Darcy's eyes.
This is invoked in the Uglies series when people decide to make everyone a generic pretty in order to resolve human conflict.
Every female character in The Name of the Wind is described as beautiful, cute, attractive, or the like. There don't appear to be any wrinkled old women running around. The next book in the series, The Wise Man's Fear, manages to avert this; several female characters are described as old or plain.
Inverted in the newspaper comic Cathy, which has a distinctive art style that renders every character either unattractive or plain-looking. To the artist's credit, characters who are ugly in-comic are unattractive in-art, but characters who're supposed to be good-looking can have Informed Attractiveness.
She also lampshaded her drawing style when her character considered getting a nose job (being famously rendered without a nose).
Garfield started out as visibly fat, but as the art style improved, he began to look pretty similar to other cats in his series (though this has the effect of making everyone look fat). Garfield and Friends starts out with this latter version, so it exaggerated his eating habits more.
Late into The Legend Of Zelda Twilight Princess, Midna refers to her cursed form as a "hideous little imp". Sure, she's a little imp, but she's more Ugly Cute than hideous. Of course, at the end of the game, you find out she usually looks like this and you might see why she calls herself "hideous".
Metal Gear qualifies - barring the occasional Gonk, everyone is distinctive-looking, but highly attractive. Even the inhuman, faceless cyborgs and robots have sexy mannerisms. Justified in that the series is a conscious attempt to make a set of games that look like Hollywood movies, so it makes sense for, say, Solid Snake and Naomi Hunter to be way hotter than a Shell Shocked Senior and a nerdy scientist would look in real life.
Fuuka of Persona 3 is said to be frail, anemic, and an unattractive computer nerd, but she has some of the most exotic looks of the cast. This is supposed to balance the almost worshipful attitude the game has for her personality, which is demure, sweet-natured and intelligent, but because she's not nearly as unappealing as everyone says she is, it comes off as more than a little silly.
It's possible that, in the English dub at least, they tried to emphasize her gawkiness through her voice acting; at times, she almost seems as though she's taken speech lessons from Half-Life's G-Man. If this was the intention, though, it seems to have largely backfired, as most players simply assume that Fuuka's voice actor can't act.
In the playable epilogue "The Answer", she sounds more mechanical than Aigis the Robot Girl.
Kaguya from Touhou could be argued to fall into the reverse category mentioned under Anime/Manga. She's supposed to be breathtakingly beautiful, but her official art isn't really any cuter or uglier than other characters'.
Further confusing the matter, drawing is not ZUN's forte.
In Umineko no Naku Koro ni, George is stated to have average to below-average looks, but looks no worse than the rest of the cast, and certainly than Battler, who is stated by Eva to be something of a looker. And this is in the novels, which feature illustrations that would be better called "generic mediocrity"—the anime makes George a full-blown bishonen with the exception of those huge glasses. Even the glasses are far more Meganekko than Nerd Glasses.
He is also supposed to be a monstrous brute who kidnaps young women, but he is genuinely fond of the girls and cares for the roc babies after he accidentally kills their mother, turning out to be a very literal Gentle Giant. Whether the DM intended this or not, Crunch subverted quite a few tropes very quickly.
Most of the cast in Questionable Content is in their 20s, the outliers being Ellen (introduced just before her 18th birthday) and Amir (35 but explicitly stated to be much younger-looking). Anyone much older than that tends to look like a younger person who dyed their hair gray for some reason.
Davan MacIntire of Something Positive is, particularly in the earlier strips, supposed to be hideously unattractive, even though he's drawn as your average geek, neither particularly handsome nor particularly ugly.
Lampshaded in Shortpacked!, where Batman has Oracle use an Enhance Button to see the face of a woman who managed to blur herself on a security tape. Didn't help, since in the DCAU all women look the way Bruce Timm draws women, i.e. attractive.
Fairly Odd Parents: Tootie is considered unattractive compared to the other girls on the show, but she doesn't appear to be anything more than a somewhat nerdy, kinda cute little girl. In the live action adaptation, however, she is accurately portrayed as being undeniably unattractive.
Meg on Family Guy is supposedly ugly and fat, but doesn't look all that different from all the other teenage girls. There's a good chance that as the resident Butt Monkey that it's entirely the point.
As many viewers have noticed, aside from attire, hair color, and being inconsistently portrayed as ever-so-slightly pudgier, Meg looks pretty much exactly like Lois, who is considered a total bombshell in-universe.
Parodied on South Park with the character "Ugly Bob", who despite looking no different than any other Canadian on the show is considered horrendously ugly by everybody and forced to wear a paper bag over his head to be considered attractive.
Lampshaded in a later episode, where Ugly Bob is shown living in America because they can't tell the difference between him and other Canadians.
They also do it to Clyde, who looks just like all the other children, but is deemed the "fat one" in the absence of Cartman.
Lucy in Winx Club is constantly teased for being hideously ugly. While her face does somewhat resemble that of the classic Wicked Witch, she's only ugly compared to her unearthily gorgeous schoolmates. However, this might just be the witches being mean.
This trope actually causes trouble in the Tom And Jerry short "Downhearted Duckling": Quacker sees a picture of a cute little duckling that looks just like him in a storybook. Unfortunately, the story was "The Ugly Duckling", so he takes it to mean that he must be ugly. He doesn't take it well.
None of the main characters of KaBlam! Life With Loopy were intending to be cute (except for Loopy, `cuz she's like, five), however Loopy's older brother Larry seems to be pretty cute according to some fans.
The Kanker sisters of Ed Edd N Eddy are supposed to be the core trio's Abhorrent Admirers. While the "unsympathetic" part is definitely well-executed, the "unattractive" part seems to be a bit far-fetched. Indeed, May, with her buckteeth, tiny eyes and protruding ears, and Lee with the manly face shape and, oh God, her feet, can hardly be considered good-looking, but Marie, if it weren't for her yellow teeth, could easily be seen as at least pretty. The designers have failed epically in making her visually unappealing by giving her the half-lidded, alluring smirk◊.
Lampshaded in an episode of Recess where Spinelli is entered into a beauty pageant (for 10 year olds). While watching all the contestants, Gretchen remarks at how similar all the girls look and they only recognise Spinelli when she shakes her fist at Ashley B.