These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Author's Saving Throw: The recent reveal that the man who was thought to be Todd Manning for eight years (the recast version, who was introduced with the reveal that Todd had plastic surgery) was the twin brother of the the original (portrayed by the original actor upon his return) is seen as such, given that many fans of the show were pissed off when the recast Todd re-raped Marty in 2008, since this means that it was a fake who did the deed.
Speaking of the re-rape, as it was called; the writers ended up resolving the plotline by having Marty team up with the other two men who raped her (who had repented and were pissed off that "Todd" (real name Victor Lord Jr.) had gotten away with raping Marty AGAIN) to basically force Victor to jump to his death in to a nearby river. In the end, Victor agreed with the three that he didn't deserve to live and jumped. Sadly, his other girlfriend Blair saved him from drowning.
Better OnDVDYouTube: Follow only the storylines you're interested in, just the teens, everyone except the teens...all that's missing is an Abridged Series.
Complete Monster: Mitch Laurence. Not only is he a murderer and a rapist, but he also recently he returned from the dead, hired two men (one her brother-in-law) to stalk his daughter and make her think her dead husband was back from the dead, then proceeded to lure her to his old home in Napa, where she found his corpse sitting there in a chair while his corpse was discovered to have disappeared from its casket back in Llanview. If the rape and murdering weren't his Moral Event Horizon, this definitely was.
Adding to that, Mitch followed that with planning to kidnap his unborn grandchild, kill its mother, and have his daughter Jessica raise it. When he found out the baby wasn't actually his grandchild, he threw its mother out in the cold, and decided the only way to get another possible heir for his creepy cult was to rape Jessica—his own daughter (or so we thought)—in the hopes she would conceive an heir. Talk about messed up.
Another one is Victor Lord, who was revealed to be a pedophile who molested his own daughter, Vicki after his first and presumed death, hence how she got multiple personality disorder. After he came Back from the Dead after The Reveal that he molested his daughter, he tried to have her heart transplanted into his failing one so he could continue his miserable existence.
It could even be argued that Victor Lord Jr was worse than Todd Manning, because while Todd was flamboyant in his evil doings, Victor was more subtle about it, making his moments of villainy more impactful.
Tess gets this as well. It doesn't matter that she's tried to kill the people that her split personality Jessica is close to, including Jessica's boyfriend and her mother, Vicki, and tries to make Jessica's life miserable. She's the real victim.
Ensemble Darkhorse & Misaimed Fandom: Roger Howarth. Originally supposed to play a short term character designed solely for Marty'sGang Rape storyline, his acting skills were quickly praised by fans, to the point that, to the writers and actor's dismay, the character of Todd recieved a lot of popularity from (girl)fans who liked him in spite of (or because of) of his crimes. One fan even held up a sign that said "Rape Me Todd!". The writers gave in and Todd was softened and given a Freudian Excuse.
In the mid-2000s, there was the John/Natalie vs John/Evangeline shipping wars.
Squick: the "rapemance" of 2008, in which amnesiac Marty fell in love with her rapist, Todd (since revealed to be his twin brother Victor).
Incidentally, this storyline was proposed years earlier, and led to Roger Howarth leaving the show, because he had a SERIOUS problem with it.
They Wasted a Perfectly Good Plot: Matthew's paralysis. Even throughout the ever-escalating Ass Pulls that the storyline took starting in the summer of '09, there was the sense that the actors were capable of, and there was support in the writers' room for, telling a sensitive, realistic story of a teen and his family coming to grips with a permanent disability; but that Executive Meddling was forcing it in the direction of wringing out as much Wangst as possible as the storyline shambled towards the inevitable miracle cure.
Revisited in the home stretch of the ABC run, in a classic cliffhanger, Matthew flatlined on a Friday, was okay on Monday.