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.
Mileage does vary. Jaxom in The White Dragon also had to put up with quite a bit of crap that he really did not deserve and also had to overcome genuine obstacles. All The Weyrs had so many problems that Jaxom was just one among many.
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 The Messiah. It was pretty blatantly clear that the author adored him, as he was talked up by everyone (except his father!) as being spectacular.
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.
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.
It's hereditary, since Bella would certainly qualify. It's hard to imagine the Scrappification of the main protagonist, but SMeyer found a way.
If heredity is a factor, Renesmee never had a chance considering even her father can qualify, especially with Team Jacob but also with... usually not fans but at least readers who don't like Jacob that much but loath Edward's Stalker with a Crush turned Up to Eleven, while the narration never neglects to tell us how great a guy he is.
Every Star Wars Expanded Universe author has favorite characters, usually their own creation, but some are more beloved than others:
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.
While Karen Traviss didn't create the Mandalorians, she did make them into a Mary Suetopia with plenty of Author 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.
It falls flat for several reasons. 1. The Jedi were far too few in number to take on the quadrillions of droids the Confederacy fielded and produced. 2. It was Palpatine and Tyrannus who commissioned the droid army using the body of a slain Master as a puppet, not the Jedi. 3. It was the Republic who fielded the clones and used them all over the galaxy during the Clone Wars and treated them as expendable tools akin to droids, while the Jedi, for the most part, tried to lead their men fairly and treat them as equals. Traviss, however, never acquainted herself with the bulk of Stars Wars Canon, and as such she wrote blatant contradictions of canon and misconceptions into her execrable novels.
Saba is turning this way, especially after Vortex and Conviction, since Troy Denning tends to take the lead role in writing these nonologies.
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.
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 Mc Kay'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.
