Shuichi Saihara became this after he turned out to be the real protagonist of the story. It didn't help that, without his hat, he has easily one of the most generic designs in the series, on top of having a personality that's similar to both former protagonists of main series; being relatively passive. Some were willing to reserve judgement on his personality and development until release, while others want his head on a skewer and feel like his role as the protagonist is an abhorrent example of Lying Creator and Very False Advertising, even for a promotional campaign that outright admitted to being misleading. Many believe that the false advertising the series is known for has gotten to the point where it's just too expected, and has long overstayed its welcome.
Adding to that, some people are also not angry at the fact that he is the real protagonist as much as with the fact that he is wimpy compared to the previous protagonists, particularly Kaede's leadership and charisma. Some fans see his Heroic B.S.O.D. and self-deprecating behavior as character depth that there wasn't previously, but others see this as a sign of Wimpification of the protagonists, worsened when compared to Maki and Kaito's pro-activeness in their Power Trio.
Additionally, Akamatsu is only playable in the prologue, Chapter 1, and two of the bonus modes where everyone is technically playable. As if to rub salt in the wound, she only has two free-time events for everyone (which is also a massive Interface Spoiler if one decides to hang out with the same character thrice) thus disappointing those who enjoyed playing as Kaede and hoped she'd have full-fledged free time event chains with everyone. It's also somewhat inconvenient, since it takes several playthroughs of Chapter 1's free time event section to complete all of Kaede's classmates' report cards.
Kokichi Oma. Many despise him for his continued antagonistic behavior and bullying towards fan favourites such as Keebo, Gonta and Himiko, his continued endangerment of the group and manipulating Gonta into killing Miu. Others meanwhile like him due to providing the morally grey character type the franchise is known for, his role as The Chessmaster, and that, while not excusable, his Moral Event Horizon was justified as Miu was attempting to kill him. Likewise, The Reveal that he was a Good All AlongAnti-Hero either works a long way towards justifying his behavior, or turns him into a posthumous Karma Houdini who gets forgiven for his continual endangerment of the group. There is also a bit of debate if he was better off as a villain or an anti-hero.
Maki is starting to skirt this territory. A lot of people are starting to dislike her due to two other fan favorites, Kaito and Kokichi, dying because of her, and would rather have those two alive than her in addition to Kokichi believing that she ended up giving the suicidal Ryoma his empty video when he wanted to find a reason to live, more or less with the intention of him committing suicide because he knew her secret. Others enjoy her character arc as well as her interesting talent, backstory and moral ambiguity as the Ultimate Assassin. They also believe that Maki didn't really actually watch his video and Kokichi's belief that she did watch Ryoma's video and gave it to him stems from his dislike towards killers. There are also several people who take issue with how her character arc revolves mostly around her relationship with Kaito.
Her attempted murder of Kokichi Oma seems to be the most divisive subject when it comes to her. Some fans believe that it was inexcusable given how everybody didn't want her to kill Kokichi and Kokichi seems to have a genuine confused reaction when Maki tells him about being a Remnant of Despair hinting that everything is not what it seems. Others believe that Kokichi stated that he was the mastermind and him being confused when Maki was talking about him being a Remnant of Despair is not going to stop Maki from thinking that he was the mastermind. Though even those who find Maki's murder attempt inexcusable believe that she was supposed to learn a lesson after Kaito ended up Taking the Bullet for Kokichi and was supposed to make a Heel–Face Turn. However, some fans believe that lesson came across as a little too late as it ended up right at the end of the game and we couldn't see if she will actually go through a Heel–Face Turn. To make matters worse she wanted to kill everybody in the fifth trial so she could survive since she thought she was the blackened, and she made no secret about how she liked the fact this would also kill Kokichi for her despite condemning her so called "friends" like Shuichi to die, and then have her be portrayed as Easily Forgiven can rub a lot of players the wrong way.
To add another layer of controversy, there has been accusations of Kodaka showing favoritism towards Maki. The Romantic Plot Tumor between Maki and Kaito can be viewed as Kodaka having a Pet OTP. While Kaito and Kokichi each represent major themes in this game such as belief and lies, and those two boys along with Shuichi can be viewed as a Freudian Trio, Maki doesn't really fit the themes of the game as much as those two. In addition to Maki being viewed as Easily Forgiven after she attempted to kill everybody, and as well as Kodaka stating a comment about him being surprised over Maki being 9th place in the official popularity polls, some fans lead to the conclusion that Maki was given too much favoritism from Kodaka.
Miu Iruma can be this especially towards western fans. People find her lewd comments either funny or annoying. In addition, the scene of her repairing Keebo has been slightly controversial as either people think it's hilarious or they dislike the idea of it being Played for Laughs. Her role in Chapter Four doesn't help much as she attempts to kill Kokichi and frame Kaito for the crime because of how she believes that "the world needs her". Others dislike her selfishness over her prioritizing her life over her classmates especially given how she would have ended up getting Keebo killed while others felt bad for her due to her motive involving wanting to take care of other citizens in the world.
Tenko's also in an odd spot with this. One of the first things known about her was how strongly she dislikes men, getting her quickly labeled as a Scrappy, but fans later learning of her excitable nature and crush on Himiko were enough to redeem her for some of them. For those who claim this isn't enough, they instead point out that her misandry not only leads her to baselessly accuse her male classmates of murder a lot, even though both of the trials she actually takes a part in have female murderers, and easily treads into both verbal and physical abuse territory, especially as her Free Time events show there is no reason for this beyond her not realizing her male "Neo-Akido" teacher was pulling her leg and some of her vigilante stunts having assumedly mostly male targets. Given how her first Free Time involves knocking Shuichi out cold over nothing that excuse can be hard to swallow and it's not helped by how little any of her classmates try to call her out on her behavior. Even her relationship with Himiko can cause issues as those less favorable towards her point out she can be pretty creepy towards the girl (not unlike Fukawa towards Togami and Souda towards Sonia) with little indication Himiko was comfortable with this at all. That is at least prior to Tenko's death, which both Kokichi and Korekiyo point out as suspicious during said trial despite how devastated she's acting and clearly misses Tenko more than Angie. Not to mention, Tenko out and out admits that she'd pick Himiko over the other students if it turned out Himiko was the murderer in the second trial.
Kaito Momota. Some fans love him for being The Heart of the group, and his Awesome Ego. Others hate him for stating some sexist comments, and his idiotic tendencies to stick with his emotions instead of logic and common sense. Not to mention his behavior in the fourth class trial where he refuses to believe that Gonta was the culprit. Some fans believe that his behavior was annoying and too OOC. Others believe it was supposed to meant to represent a Fatal Flaw in Kaito's characer. Also, some fans thought that he was acting incredibly petty towards Shuichi for revealing the truth that Gonta committed murder despite knowing that if group voted for Kokichi instead like Kaito wanted (and assumedly did by himself anyway, given how the votes are revealed) they would have all died.