Cassie from the Animorphs. She's the stated favorite of writer K. A. Applegate, she is the only character in-series to win the Superpower Lottery (being both an estreen and a temporal anomaly) and she is usually praised and defended by the narrative even when it's completely unwarranted - take for example Megamorphs #02, when Marco privately compliments Cassie for going on a whiny rant about killing a Triceratops, or #53 The Answer, when Tobias harshly criticizes Jake for excluding Cassie from the war council despite the fact that he had extremely good reason to (that reason being that she betrayed the whole team by allowing the blue box to be seized by the Yeerks, and all for a 'gut feeling' that she's lucky to see pan out). She criticizes the others from start to finish, puts the whole team at risk on multiple occasions to justify her extreme sense of morality, and she is the only character to never learn or grow in any way. This even extends to the epilogue, where she is the only Animorph that Applegate spared from the Bolivian Army Ending.
Her EverworldExpy, April, may qualify as well. She is endlessly self-righteous and, out of the main cast, she's the only one who never has to undergo any major suffering from her own character flaws which, like with Cassie, are glossed over or ignored.
Karen Brewer from the Baby Sitters Club. She was annoying, rude, a know-it-all prone to causing trouble because of it... but never got called out on her behavior because she was a self-admitted Author Avatar for the kind of "bright, imaginative" kid the author had always wanted to be. Thus Karen even gets her own spin-off series. Except apparently the author was pretty much alone in her desire; it'd be hard to find even one fan of the series that actually viewed Karen in a positive light.
Renesmee from Breaking Dawn. Everyone who meets her loves her, despite the fact that she hasn't done anything other than be Edward and Bella's half human/half vampire daughter with psychic powers. Many fans loathe her for hijacking the story away from the Official Couple. Others hate her for her very existence defies biologyand is a direct contradiction to previous Word of God. And of course, Team Jacob fans hate her for otherreasons... It certainly doesn't help that it's obvious this is a motherhood fantasy with how thanks to her vampire nature, Renesmee's super-smart and beautiful and loved by everyone who meets her, but Bella doesn't have to deal with any of the gross/boring/hard parts of being a parent. Not only that, it looks very much like she and children who were turned into vampires have a supernatural ability to make people love them, but it's entirely accidental. The reader is supposed to take it as a given that vampire and half-vampire children, Renesmee especially, are just that lovable.
In the Casson Family Series by Hilary McKay, Rose Casson gradually gets revealed as this over the course of the series. At first they seem like an ensemble series, with each book focused on a different member of the family with the others getting their own subplots...but then Rose not only gets more books with her name in the title than anyone else, she also starts taking over the books of OTHER characters, so much so that Caddy is basically a minor character in her own book. Especially blatant evidence of McKay's Rose favoritism is that every time Tom is mentioned, it's in relation to Rose—despite him being established as INDIGO'S best friend in the first book he appeared in.
Karen Traviss rears her head for the second time on this page with herinclusionsto theHalo novels, this time with Admiral Parangonsky and Serin Osman. Usually, anything they say is right and is a mirror to Traviss' own beliefs, at the cost of shattering canon relationships, butchering how psychology works, and ignoring the military chain of command.
In S.D. Perry's Novelizations of the Resident Evil series, she took plucky little RebeccaChambers and made her into her go-to hero, even receiving a spinoff novel all to herself — Resident Evil: Caliban Cove, which itself received a sequel in Resident Evil: Underworld. Basically, if something is happening in the plot, Rebecca is doing it; if something is not happening, the characters described will be going on at length about how wonderful/resourceful/intelligent Rebecca is. (It's kind of like the films except focusing on Rebecca, not Alice.)
Kevin J. Anderson has Kyp Durron, a slave raised on the penal colony of Kessel because his parents were Rebel sympathizers. Han Solo finds him, and discovers that he's more powerful than Luke. He then becomes Luke's brightest student, but The Paragon Always Rebels and he does so in a big way, rending Luke's soul from his body and stealing an invincible Imperial planetkiller that he stole from the Empire in the first place, and turning it on a system with an Imperial training academy. He then demands to see his brother, but they can't find his brother, so he blows up the star. And they find his brother and release him to Kyp, but he doesn't get to the Sun Crusher in time to be protected. And when Luke recovers, after The Power of Friendship destroys the evil Sith Lord influencing Kyp, the New Republic grants him the power to determine Kyp's fate, and Luke forgives him. Although, after I, Jedi pointed out the massive problem with this (among other decisions Anderson made), rare was the appearance of Kyp where someone didn't point out "Dude, you killed a solar system.
Stackpole has Corran Horn. The author repeatedly shoved Horn into the background of other authors stories, and in the case of the Jedi Academy Trilogy, completely subverted its tone in the I, Jedi book. He repeatedly has major lore characters (Wedge, Han, and Luke for starters) singing Horn's praises.
While Karen Traviss didn't create the Mandalorians, she did make them into a Mary Suetopia with plenty of exposition. You'd think that she points out the He Who Fights Monsters aspect of the Jedi making clones to fight their wars would go in her favor, but with how perfect the Mandalorians are, it doesn't.
Saba is turning this way, especially after Vortex and Conviction, since Troy Denning tends to take the lead role in writing these nonologies.
Elizabeth Wakefield from the Sweet Valley series is purported to be the good twin who is nice to everyone - but, more often than not, she comes off as a sanctimonious hypocrite. As such, many find her to be even worse than the allegedly bad twin, Jessica.
Lord Jaxom from the Dragonriders of Pern series. His high Gary Stu levels were barely acceptable in The White Dragon. But when he was made the focus character in All The Weyrs Of Pern - which featured the resolution of F'lar's dream of removing the threat of Thread permanently - the fandom turned on Jaxom en masse.
Todd Reeve in "Decision at Doona". An anti-social six year old who knew everything. Once he got out of the over-populated corridors of Earth and into the wild of Doona he was such a "natural genius" he was practically a Messiah. It was pretty blatantly clear that the author adored him, as he was talked up by everyone (except his father!) as being spectacular.