One of many, many reasons that Berry Shirayuki from Tokyo Mew Mew A La Mode is so unlikeable. What's more, Executive Meddling took it all the way - Ichigo's powers mysteriously mutated, so she functions as Berry's powerup item and nothing more.
Aguri/Cure Ace of DokiDoki! Precure for replacing the well liked Regina, who the show was leading up to her making a Heel-Face Turn and becoming a Cure. Made worse by the fact that she breaks tradition of a previously established character becoing a Cure by being a new character that we've never seen before.
And also to the new versions of the Knight Sabers in Bubblegum Crisis: Tokyo 2040.
Probably the biggest reason many Mobile Suit Gundam SEED Destiny fans hate Shinn Asuka is that he's not Kira. The fact that Kira is still a member of the cast does not help, and a few fans don't even consider the Hostile Show Takeover to be enough, stating that the series needed to focus on Kira from the earliest possible moment.
It should be noted that a fair portion of the fanbase simply dislike him based on his Jerk Ass attitude, his blaming others for everything and that he never admits to his own mistakes. Not exactly the most endearing of protagonists, even in a franchise that includes similar whiny jerks Amuro Ray and Kamille Bidan.
Subverted by Tengen Toppa Gurren Lagann. After Kamina's death, a lot of fans freaked out when they heard that he would be semi-replaced by Nia. However, by the end of her three-episode-long introduction, she had gained a level of popularity rivaling that of the original three, and as more Woobie-tasticCharacter Development followed, her popularity finally equaled that of the original Power Trio.
Also flat-out inverted in the last act of the show, when Viral pulled a Heel-Face Turn to become Gurren's pilot, which was most likely because of the character's existing fanbase.
Sai, who replaced Sasuke Uchiha on Team 7 in Naruto, was hated by two groups of fans. Sasuke fans that hated the idea of someone replacing him. And Sasuke haters who didn't take to the character and even saw him as worse than the guy he replaced. However, Sai proves to be quite different. Sasuke has always been portrayed as the non-smiling stoic and so most fans probably assumed Sai would play the same role. Instead we have someone who always smiles, cracks jokes about Naruto and expresses how he feels from the get-go as opposed to staying silent and generally is shown to be less and less like Sasuke.
In-universe, Naruto himself says at one point that he can never replace Sasuke.
Madara never gets the end of it from people who can't accept anyone but Orochimaru as the final villain, or who were disappointed that the apparent leader of Akatsuki until then, Pain, was not the main villain either. And it turns out that Madara is not the main villain either! Or at least the series is not going in that direction.
In the Pokémon anime, some people disliked May because she replaced Misty. Although in the previous arc, Misty's character was largely changed by the introduction of Togepi, who is a major Scrappy in his own right for this reason; fans mainly remember Misty at her peak for being a strong and dedicated female character, whereas May was portrayed as more of a stereotypical girl. (It didn't help that most of her Pokémon were arguably feminine and she was drawn with an oversized chest.) However, May eventually gained a large fanbase of her own, and come next arc, some people disliked Dawn because she replaced May and/or Misty.
A good number of fans hated Tracey for replacing Brock, some even making up reasons like "he's a fat pervert" to justify this. (Incredibly stupid considering that Brock, himself, is a blatant pervert.)
Iris originally suffered this before Best Wishes came out, not because she was replacing Dawn but because she wasn't the female protagonist of Black and White. Fans wanked her as being a racist character but the tides eventually settled almost immediately when she was revealed to be the last Gym Leader of Pokémon White who could use powerful dragon Pokémon. So, unlike Dawn who was seen as a Replacement Scrappy from the very beginning, it disappeared concerning Iris for the most part.
Finally, Paul fans see Ash's new rival Trip as one because, "He's not Paul." The creators are obviously not aiming for another Paul type of character and Trip is seen to be completely different as he's nicer to his Pokémon, does try to help Ash and Iris out on occasion and is not a poor sport like Paul demonstrated himself to be at the beginning. Paul's fans don't care.
An unusual outlook, seeing as how Paul is often considered a total Replacement Scrappy of Gary Oak. Both were skilled trainers who focused on strong, rare Pokémon. The difference being that Gary had an arrogant, boastful personality, and Paul was more dark, serious and overly dramatic.
To give a better example, at the start, everyone complained that he was too invincible for a rookie trainer due to beating Ash twice (the first battle shouldn't count though), but currently, now that he's suffering some losses, they complain that he's not a worthy, interesting rival for Ash at all because he's too weak! At this point, it's more likely that these fans just hate Trip for replacing Paul, and will complain no matter what he does and given Paul's fanbase, it's not going to go away.
Pet Shop of Horrors: Tokyo, which follows Count D at his new Little Shop That Wasn't There Yesterday in Tokyo, introduces Wu Fei to fill the role held by Leon Orcot in the original. Many fans who are less than pleased about Leon's absence from the new series are rather disenchanted with Wu Fei as a result.
Ranma ˝: Sasuke the Ninja, who replaces Hikaru Gosunkugi in the anime adaptations of the latter's first appearances. Even if it doesn't really make sense, such disguising oneself as a balcony just to be near Akane during a Romeo & Juliet play. Instant Awesome, Just Add Ninja didn't work.
In regards to Gundam 00, Lyle Dylandy aka the second Lockon Stratos might become an in universe case, at least in regards to Tieria Erde, who has to remind himself that this Lockon isn't his dead first love friend and teammate Neil Dylandy, the first Lockon * and* Lyle's older twin brother. And fandom sees to be prone to bitch him out a bit as well... We'll have to see how it goes, though.
After he drops his nonchalant facade and shows genuine emotions as he witnesses the destruction of the Kataron HQ, people are a bit more forgiving...
A good portion of the fanbase also dislikes Lyle due to the fact that he spends most of the series being almost an exact clone of his brother, to the point of giving up his human identity to become his brother's role at the end even though a crucial point of his character lay in the fact that he was supposed to be his own person and more than just a Backup Twin. A few attempts are made to Hand Wave the writers' laziness but they are either rushed through as in the case of his relationship with Anew) or are subplots which are never elaborated upon (like his involvement with Katharon) except in sidematerials released alongside the show.
Lyle has been forgiven for the most part due to elements of plot settling in and realizing the differences (for unlike his brother, he continues his Gundam Meister role without hatred in his heart), and his scenes in the movie, showing that even in combat he's different from his brother (Favoring Gun Kata , Beam Spam, or Drone Attacks to traditional sniping)
Mileina has received a little bit of this as well for replacing the lovable Christina Sierra.
Plenty of Nanoha fans were upset with season 3, when Yuuno and Chrono virtually vanished, and the four new characters were given so much facetime. It was necessary to insert most of these characters for the later plot twists. But still, lots of griping about Subaru and Tea.
As suggested by the quote on the page, in Code Geass Rolo Lamperouge becomes a Replacement Scrappy in-universe for Lelouch after Lelouch discovers that Rolo was sent to replace Lelouch's true sibling, Nunnally.
This eventually changes when Lelouch accepts Rolo right before he died, though even then he only accepts him as the brother of "Lelouch Lamperouge", and not of "Lelouch Vi Britannia."
What Lelouch means by making that difference is that, although they are not related by blood (Rolo is not a vi Britannia and he didn't share Lelouch's childhood as a prince either), he should have realised sooner that they were indeed brothers anyway (symbolized by the surname Lamperouge, which is equally fake for both and also refers to the time they spent together living happily as ordinary students).
Patlabor After Kanuka's time with the SV 2 guys is up she goes back to the US and is replaced by one Takeo Kummagmi. Who is overall less than impressive.
In Bakuman。, Miura got this in series from the main characters for replacing Hattori as their editor. Mashiro and Takagi preferred not to go into gag manga, while Miura preferred to make more humorous series, partly as a result of a desire to have someone under him get serialized, leading to a few arguments until they managed to work out their issues and get along better together. This also happened when he replaced Hattori (again) as Iwase's editor, and this was particularly infuriating for her because she'd been attracted to Hattori.
Zelgadiss and Amelia's replacements in the Light Novel series, Luke and Millina, are no where near as loved or popular as they are; compared to the former two, Luke and Millina have virtually no established background, no Character Development, and are exceptionally bland personality wise: Luke is a less outspoken Expy of Lina, while Millina is a perpetual grouch, and a Satellite Love Interest for Luke. The greater majority of fans outside of Japan have most likely never heard of either of them, and even in Japan they get little love. Case in point: three of the Slayers Special light novels (the prequel to the main series) have side stories for Gourry (Lina's lancer in the books), Zelgadiss, and Amelia; none exist for Luke and Millina.
The voice actors for the ADV Films dubs of the movies, especially Cynthia Martinez as Lina, are widely disliked. Also, when Crispin Freeman replaced Daniel Cronin in the first season, he was disliked because of his more "vibrant" voice, but now the opposite (dislike of Cronin's voice) is true. When Veronica Taylor began voicing Amelia, however, she was considered to be a huge improvement.
Tenchi Muyo! fans were angry that the role of 'Mihoshi's partner' was passed from Kiyone Makibi to Noike. Noike is hated for a lot of different reasons, but this is the main one that comes up.
Another in-universe example comes from Gundam 0080, where the Cyclops Team members are pretty open in their dislike for Bernie, who was assigned to them shortly after they lost a long-time member of the team.
Near and Mello in Death Note, who replace L (particularly Near, who gets the official job.) Made worse by the fact that their appearance coincided with a massive change in the setup of the manga. Light's in charge of the investigation, detective cat and mouse games take a back seat to a more political game, and the overt Foe Yay between L and Light never develops an equivalent with the new characters. Also, the distribution of victories between the sides of Kira and L are drastically different and more one-sided.
Or more specifically with the Foe Yay, it too becomes one sided and distictly rapey too, with Near obsessively calling him and then hanging up, the very strange faces he makes while thinking about Light and the reveal in the manga that he wants to KEEP him.
A lot of Weiß Kreuz fans were not impressed by Izumi Sena taking over Omi's role as the youngest and most idealistic member of Weiss in Weiss Kreuz Gluhen. Interestingly, there was much less backlash against Chloe in the Weiss Side B manga, in spite of the fact that he took over Yoji's role in the team.
Dragon Ball Z gives us a weird example when Main Timeline Trunks. The Trunks introduced in the Android saga was a Badass from a dark future whose experiences had humbled him and made him serious and fans liked him. But when history changed so that the androids were defeated the Trunks of the main timeline was allowed to grow up with both his parents and came off like a spoiled brat.
The wraiths in Puella Magi Madoka Magica are this to the witches, since they became the analogue for witches when Madoka remade the universe to erase them. Despite their importance to the series, most fans find them to be boring and ugly in comparison to the highly varied and characterful witches, especially given that the series is pretty vague on just what they are (since they only appear for a few minutes in the last episode). Many a writer has grumbled about having to use wraiths in Continuation Fic, often creating whole reams of fanon to make them more interesting or just writing non-action WAFF. Even the staff seems to dislike them, placing them Out of Focus in nearly all official material.