Lotta Hart, a tabloid photographer with a Southern accent who appears in three cases in the series, much to the dismay of her haters. It doesn't help that whenever she appears, she takes some sort of photo of something involving the crime, and these photos are always horribly misleading.
Spark Brushel in Apollo Justice. It doesn't help at all that his Perception tic is a Guide Dang It; specifically, it's a sweaty armpit, not where most people would even think (or want) to look.
Not to mention Wendy Oldbag, although even in canon she's supposed to be repulsive. Although Oldbag IS surprisingly popular in Japan.
The above also applies to Larry, which is amusing because they've shown up together twice. Even in canon people try to avoid being around him, but he's constantly popping up in nearly every game.
Many fans consider Mike Meekins to be the worst of the worst, due in no small part that he talks through an ear-screeching megaphone every few seconds. Thankfully, he ditched the megaphone in Ace Attorney Investigations, but many fans still hate him for being obnoxious and stupid.
Zinc Lablanc II, the loudobnoxious art dealer from Ace Attorney Investigations who constantly sticks his nose into the investigation. Despised so much that players were wishing he was the murderer just so he can be arrested or totally not minding if his fall ended in with his death (and neither does any of the characters but Gumshoe).
Also from Ace Attorney Investigations, Calisto Yew. It's difficult to find a fan who doesn't find her annoying. Also, Being Shih-na hasn't helped her gaining fans.
Shinji Matou. His crimes are numerous: He's a self-serving Smug Snake who treats his friends like garbage, and a weak magus but thinks himself too great and forces his way into the war... by forcing Sakura to yield Rider to him, and treats her like garbage anyway, calling her weak at times despite him actually holding back her true powers. He still scolds and abuses Sakura a lot for 'staying' with Shiro, even raping her (maybe Rider too) on a daily basis to vent his frustration. It doesn't help matters that in the only route which sets out to redeem him (the UBW route), he arguably becomes worse than in any other story path, what with him cruelly ordering Gilgamesh to rip outIlya's heart, laughing as he watched it happen. The only reason he even does a Heel-Face Turn at the end of this route is due to a serious round of Break the Haughty, and considering his previous actions the fact that he doesn't need to actually do anything to redeem himself makes Shirou's - and the story's - claims that he's become a better person fall flat as a result.
In Heaven's Feel, when he is killed by Sakura in self-defense, it seems that he broke from the strain of being the end of the magic in the Matou/Makiri bloodline long ago, so it's actually possible to feel a bit of pity for him.
Zouken Matou generally gets tons of hate as well - he's considered so thoroughly despicable with such dreadful deeds to his name that his Freudian Excuse - abeit a pretty weak one to begin with - earns him next to zero sympathy from the audience despite being a legitimate one (there's only so far a reason for being a Jerk Ass can actually justify one's bad behaviour, after all). Sakura fans in particular despise him. His Servant, True Assassin is also widely disliked - being limited to a single story path (Heaven's Feel) and not getting much characterisation tends to do that to you. True Assassin is mostly regarded with apathy rather than outright hate, and does have his fans, but nonetheless doesn't win points for being, to some, a Replacement Scrappy for the first, 'Fake' Assassin, who is a fairly well-liked character in his own right and needs to be eaten to bring True Assassin (whose I'm a Humanitarian aspects are also frowned upon) into the picture.
Not helping True Assassin is how pathetically weak he is. He only managed to truly defeat one Servant, and that was only due to that Servant being cornered by a foe that even Berserker and Gil couldn't defeat while on very unfavourable terrain. Fake Assassin was at least able to keep up with other Servants, even being able to hold back Berserker, and could possibly even be able to defeat a strong Saber if he didn't want to rush the battle's end.
From the start, Maria is an annoying problem child. She throws temper tantrums when she doesn’t get her way, screams obnoxiously at every opportunity, and frequently goes into a full blown Creepy Child mode where she cackles manically, arrogantly flaunts her knowledge of magic, and shows little care for all the deaths happening around her. Unsurprisingly, she rubs many fans the wrong way. Unfortunately, almost nobody in-universe likes Maria much either. Her mother frequently beats her at the drop of a hat, everyone picks on her at school, her cousins look the other way at her abuse, and her only friends are either imaginary, or as broken as she is. By the time we’re treated to a fantasy sequence where she imagines herself brutally tearing her mother apart, it’s hard to know whether to be disturbed or to cheer the poor girl on.
George also gets this reaction for his creepy treatment of Shannon, sexism, and borderline Yandere tendencies. This doesn't even take into account the Rosatrice Culprit Theory.