There are subjectives, and then there are these. While you may believe a work fits here, and you might be right, people tend to have rather vocal, differing opinions about this subject. Please keep these off of the work's page.
LLSmoothJ: Speaking of Joey, the KaibaCorp Grand Prix treats him even worse as he becomes the butt of a joke based on a card in Yugi's deck (which even his friends laugh about). Even worse, in the tournament, his decline continues as he loses within the second round (I know it was to the Big Bad of this arc, but still, Joey was supposed to have become incredibly strong post Battle City, and the arc's Big Bad wasn't the kind of person who should be flooring him that easily) of the tournament (he won the first round against Yugi's Grandpa, which may bring up a debate whether he let him win or not). It's bad enough he was already made into theKrillin of Yu-Gi-Oh, but now the Yamcha as well? Make you wonder if Joey's treatment is to pander to Kaiba's fanbase. Protip, writers: When you make a character into the second-most important person in the series, you must treat him accordingly. You don't give him second chair to fucking Seto.
Dashguy: On the topic of Character Derailment in the DOMA arc, there's Yami Yugi's duel against Raphael. To make it short: Raphael gets the upper hand, gives the "Seal of Orichalcos" card to Yami Yugi and tells him that since he's "evil" he has to use that card. Note that, at this point, the only danger in dueling came from the above mentioned "Seal of Orichalcos" card which would drain the soul of the loser; so you would expect Yami Yugi to tell Raphael to fuck off and keep playing right? Nope. He uses the card, loses and Little Yugi ends up sacrificing his soul in his place. This is a case of Aesop Amnesia, with reference to the lesson Yami learned about winning at all costs back in Duelist Kingdom.
RAZ: Speaking of the DOMA story, the one real Dethroning Moment for me is the ending battle against the Leviathan. Okay, so Yami Yugi's awakened the three Legendary Knights, the ones that are supposed to be able to destroy the beast, right? Wrong! They get completely curbstomped and eventually destroyed so the Egyptian Gods can come in for the final battle instead, meaning the entire purpose of the Knights was utterly friggin pointless! Oh, but it gets better: right before the battle, both Kaiba and Joey had their souls recovered after previously losing them and return to aid Yami Yugi. So awesome moment of them delivering some payback for nearly being absorbed like the other duelists all were? Not so much, because the attacks from their own monsters get shrugged off and they both eventually wind up getting absorbed by the Leviathan anyway! So... what the hell was the point of reviving them in the first place if that's all they were going to amount to?!
EDP: For me Kaiba's dethroning moment comes during his duel with Yugi at the Duelist Kingdom: when Yugi was about to defeat him, Kaiba declared he'd take a step back for any 100 HP he'd lose to try and convince Yugi to not attack and gain the turn he needed to win... But he had the Negate Attack card deployed, meaning he could have negated Celtic Guardian's attack and get his turn to attack without playing drama queen.
Brendan D Rizzo: In my opinion, the dumbest point in the original anime was the start of the second Virtual World arc. Not only was it placed in probably the worst possible point of the series (putting a Story Arc within another story arc is just stupid and serves no purpose but to stall the original arc even further) but the real reason it qualifies for this status, in my opinion, is that the villains have absolutely no reason to fight the heroes using a children's card game, but they do so anyway. At least in Duelist Kingdom and Battle City this made sense, since those arcs were both Duel Monsters tournaments, but here? The Big Five and Noah (and Gozaburo) are trying to regain control of KaibaCorp. by committing Grand Theft Me. How in Horakhty's name would losing a card game allow them to do this? The source material isn't anywhere near as monomaniacal about a single game as the anime turned into, and this arc marked the point in which Duel Monsters shifted from "one game among many" to "the only thing that matters in the universe". At least I can take comfort in the fact that it was Filler.
Valkir: Despite featuring Akiza Izinki in a fairly positive light, the finale to the Team Unicorn duel tainted 5Ds beyond all recognition. Yusei is down to no cards in his deck and all Jean needs to do is end his turn for a win, delivering the first true loss to an otherwise Invincible Hero. All this time, Jean's team has been all about using team strategy for the good of everyone. But Jean is suddenly...er...passionate about his duel with Yusei and suddenly feels the need to attack him, which his team inexplicably supports. He runs into a defensive monster that Yusei boosts with Fortress Warrior and Yusei pulls away with a win despite deserving to lose in every single way. We're supposed to believe that team victory between three people that are extremely cohesive and genuinely care about one another is less important than one superstar flexing for his friends, despite that the former resonates with the themes of the franchise far more than the latter. Yusei's plot armor actually hypnotized Jean into losing. "End your damn turn, Jean" has become synonymous with "jumping the shark" in the fandom. The worst part? It wasn't singles elimination, so Yusei's team had no story requirement to win at all...they could've won their next match and still stayed in the plot.