The character Priss from Bubblegum Crisis was originally going to be killed off and replaced by Vision, who was suspiciously similar (brown hair, kind of feisty, was a singer) but ultimately fans liked the character, so she wasn't killed off after all, thus avoiding the trope entirely.
Corpse Princess's Keisei dies, allowing Ouri to come closer to Makina and to also be brought into the story as a major player instead of a male damsel in distress and hapless bystander. About 2 episodes later Keisei's mentor is introduced. He has a very similar hairstyle and replaces the former as the even more perverted comic relief and Ouri's new mentor.
Vincent Volaju is one for Vicious in the Cowboy Bebop movie.
After Tup Dop, a supporting character of D.Gray-Man was killed, he was replaced by his equally chubby and androgynous sister, Cash Dop.
Near from Death Note. This is intentional — Near tries to imitate L and eventually admits that he failed to imitate L, but succeeded through Teeth-Clenched Teamwork. The reasoning in the story being rather interesting, Near has more tendency to 'cheat' in his methods, the example being that if he were in L's shoes, he'd have released all information on the Death Note to the public and let the ensuing mass manhunt capture Kira. He tries to imitate L because he knows that in the real world, his methods would cause far too much collateral damage even if they succeeded.
Tomboyish teen sleuth Masumi Sera from Detective Conan was created as a replacement for Natsuki Koshimizu, a tomboyish one-shot detective from earlier in the series. According to Gosho Aoyama, Masumi was created because Natsuki had become unexpectedly popular with the fans, but the fact that she killed someone and was subsequently arrested for the crime made it impossible to use her in future stories.
Each season'slancer is a Suspiciously Similar Substitute of Yamato from the first season. He, Ken/Digimon Kaiser, Ruki, Kouji, Touma, and Kiriha are varying degrees of blue oni to the Goggle Boy's red oni, each has some connection to the color blue, all but Ken and Kiriha are partnered with or transform into canids, and three of them are blond males. Kiriha's an odd duck, though, as he is partnered with a Greymon, traditionally associated with the Goggle Boy. At least it's blue this time around.
Dragon Ball Z: Akira Toriyama planned on having Goku and Vegeta fuse during the Buu Saga; however, at the time Dragon Ball Z: Fusion Reborn was about to come out and one of the film's big selling points was that it was going to be the first appearance of Goku and Vegeta's Fusion, Gogeta. Not wanting to step on Toei's toes, Toriyama invented Vegetto, who's created when Goku and Vegeta use a completely different method of fusion. Interestingly, Vegetto seems to have become the "official" fusion, appearing in the manga and Dragon Ball Super while Gogeta remains in the dubious canon territory of Fusion Reborn and Dragon Ball GT (though of course, both appear in video games).
The villains from most of the DBZ movies are stand-ins/retreads of villains from the original manga: Garlic Jr. is a much more menacing Pilafnote They even share voice actors in several countries, including the original Japanese and both Funimation and the Ocean Group's English dubs, Tullece copies Vegeta (while also being a take on "What if Goku had stayed evil?"), Lord Slug is a transparent copy of Demon King Piccolo, Cooler is (obviously) a copy of his younger brother Freeza, and Janemba is a riff on Majin Buu. Android 13 has some vague similarities to Cell, mostly in that he absorbs parts from his "brothers" to assume a more powerful form.
After performing a Heroic Sacrifice in Getter Robo, Musashi was replaced by a new pilot named Benkei. Across the various iterations of the franchise, both characters tend to have a similar pattern of being a fat Butt-Monkey who is prone to injury and death. They're so similar that at least one adaptation cut out the middleman and made the two of them into a Composite Character.
In Mobile Suit Gundam 00Neil Dilandy, killed late in the 1st series, is replaced by his twin brother Lyle Dilandy.
In Naruto, Sai, the quiet, serious and emotionally distant ninja replaced Sasuke, the quiet, serious and emotionally distant ninja. It doesn't help that they look so similar, either. Much like Sasuke during the early arcs, Sai's rocky friendship with Naruto and Sakura has slowly eroded his stoicism. The similarities between Sai and Sasuke have been lampshaded in-series. During his introduction this was played for drama, with Naruto and Sakura openly hostile at Sai attempting to replace Sasuke. Afterward it was played for comedy, such as Konohamaru's use of both Sai and Sasuke in his male version of the Sexy Jutsu.
In Patlabor, Takeo Kumagami replaces Kanuka Clancy after Clancy returns to America. They have very similar skills and fulfill the same police positions, although Kumagami is given a few quirks to distinguish her.
The female coordinator character May (who replaced the significantly different Misty) was replaced by the female coordinator character Dawn.
Dawn was then replaced by Iris, who in a roundabout way, is actually closer to Misty in terms of personality. Iris would later be replaced by Serena, who also has a personality similar to May and Dawn.
Brock was replaced with Cilan, who is the same with more food focus and less lechery. Cilan was later replaced by Clemont (another gym leader who became fascinated by Ash's battle style and the resident Team Chef).
While it skipped several years, Bonnie is essentially a Distaff Counterpart to Max. Her relationship with Clemont is similar to May and Max's, with the biggest difference being the genders reversed.
Ash's classmates in Sun and Moon share many elements with his companions from past sagas. For example, Lana is associated with Water-types and is an avid fisherwoman, much like Misty and Sophocles is a Gadgeteer Genius who has an affinity for Electric-types, kind of like Clemont. At the same time though, they have unique traits that set them apart from the character they're generally based on, which makes this a Downplayed Example.
Jessie and James release their Victreebel (a carnivorous plant Pokémon) and Arbok (a poisonous snake Pokémon). Later on, James acquires a Cacnea (a cactus Pokémon) and Carnivine (a carnivorous plant Pokémon), which both retain Victreebel's tendency to accidentally injure its owner in displays of affection, and Jessie gets a Seviper, which is...a poisonous snake Pokémon.
Ash gets a new bird Pokémon in every region which eventually is fully evolved (Pidgeot, Noctowl, Swellow, Staraptor, and Unfezant respectively).
The Mewtwo that appears in Genesect and the Legend Awakened is a different one from the one in Mewtwo Strikes Back and its direct sequel. However, despite a slight change in personality, voice and abilities, it functions almost exactly like the original, and little justifies the existence of this new one (in and of itself a bizarre choice as prior to this it was universally depicted as a Single Specimen Species). Made even more apparent considering the prologue dedicated to it gives it almost the exact same past as the old one, but with all things Team Rocket related removed, and the film's ending, which puts it in a city... which is exactly where we last saw the original Mewtwo.
The 1998 Japan-only radio drama It's A White Tomorrow, Team Rocket! introduced a Team Rocket trainee named "Mondo". Years later, an extremely similar looking ex-Team Rocket member named "Yusaku" ("Christopher" in the English dub) appeared as a Character of the Day in Sinnoh.
Saint Seiya: Lyra Orpheus was popular in the first movie and so later on in the Hades Saga, Lyra Orphee was created with the exact same backstory, lover, Cloth and hair style except he wasn't as dark and wasn't a villain.
Tenchi Muyo! is unique in that the third OVA did something of an alternate continuity substitution. Mihoshi's partner in the Galaxy Police had long been Kiyone Makibi in the Universe and Tokyo continuities, but supplemental materials Kiyone was the name of Tenchi's Mother (The first movie, based off the first TV series, named her Achika). OVA 3 introduces us to Noike, who happens to be Mihoshi's previously not known to exist GXP partner, while Tenchi's mother is finally officially named as Kiyone (and (re)introduced, in a way, by Tenchi's older sister who is strangely identical to her).