You're making a copy of yourself, for whatever reason, but while you're at it, why not make some improvements?
Accelerated maturation might shorten the time you have to wait, enhanced strength might make better workers or soldiers, super smarts might help them with your research, or maybe that "free will" thing is too troublesome for your liking.
Anime and Manga
- A Certain Magical Index: The MISAKA series are a Clone Army based on the teenage Misaka "Railgun" Mikoto, one of the world's strongest espers; while their electric powers are far inferior to the original's, they receive "programming" at birth which allows them to link their brainwaves into a Hive Mind (which was in fact the true reason for the project, as there are a lot of ways to abuse such a large mass of psychic energy). Much later, the series introduces MISAKA Worst, a clone that's been aged to around sixteen and modified into a Super Soldier; Worst's powers are much closer to the original's, though she mostly uses them to create explosions.
- Most clones in Lyrical Nanoha are modified in some manner, even before Clones Are People, Too is factored in. Almost all of them are more powerful mages than their originals and the combat cyborgs in particular have been adjusted to keep their bodies from rejecting all their mechanical implants.
- In the Futurama comic "The A-Team", the crew meet a Zoidberg clone who has hair and is apparently "better" than the original.
- Spider-Girl: April Parker was a clone of May Parker spliced with a sample of the Venom symbiote, allowing her to shapeshift and transform into a monstrous form.
- Superboy (1994): Originally the Kon-El/Conner Kent Superboy was a clone of the amoral scientist head of Cadmus, Dr. Paul Westfield, modified to have telekinesis that mimicked kryptonian powers after Cadmus' twelve previous attempts to clone Superman failed. By the time of his second series he'd been reimagined as the half-human-half-kryptonian "clone" of Lex Luthor and Superman, which was not a huge swerve as Lex's interference with the project that created Kon was well established from the get go.
- The Mania symbiote is a modified clone of the Venom symbiote, created by the Ararat Corporation from a chunk of the latter's tongue. It was supposed to be reabsorbed into the original and overdose it with reproductive hormones, but that never happened and for the most part it was identical to the original, though in Venom Inc. it temporarily developed the ability to control people using pieces of itself.
- The original Anti-Venom symbiote was created when Eddie Brock's Venom codex — trace remnants of the symbiote left in his body — were infused with Martin Li's lightforce energy, fusing them to his white blood cells to create a mindless symbiote with healing abilities, a touch caustic to normal symbiotes, and none of a normal symbiote's weaknesses.
- Several authors of Wonder Woman present the titular character as essentially a magically created clone of her mother Hippolyta with added boons of power from Aphrodite, and/or the other goddesses with have been associated with her creation over the various reboots.
- Laura herself was modified by necessity. The genetic samples salvaged from Wolverine were severely damaged, leaving only the X chromosome intact. As a result, attempts to create an exact clone of Logan failed. Sarah Kinney, the program's lead geneticist, instead proposed modifying the clone by duplicating the X chromosome, thus making a female.
- In the Circle of Four, Blackheart - the son of Mephisto - created four clones of X-23 and bonded them to samples of the Toxin symbiote.
- A recurring subplot of All-New Wolverine and X-23 Vol. 4 is Dr. Chandler's attempts to duplicate X-23, first with the Sisters, and later with the X-Assassins:
- The Sisters (except for Gabby) failed to develop the X-gene altogether due to flaws in the cloning process, making them an unintentional example of this trope. Additionally, Bellona was further modified when these same flaws led her to develop albinism. More intentionally, all of the girls were rapid-aged to maturity.
- The X-Assassins were modified by completely eliminating their Healing Factor altogether, attempting to bypass Laura's pesky morality by making them disposable cyborgs. Further experiments building off the same project led to Laura's DNA being used to create genetically modified...turkeys.
- In Calvin and Hobbes, after Calvin's first attempt at cloning went predictably awry because he couldn't control his clones, he installed an ethical switch on the duplicator and made a clone of his good side. The clone eventually poofed when he threatened Calvin with violence over their irreconcilable views on Susie.
- The Clone Army in Attack of the Clones are modified to age at twice the normal rate, and follow orders practically without question. Their genetic template, Jango Fett, commissioned an unmodified clone to raise as a son, Boba.
- In the Liaden Universe series, a character called The Uncle has survived for hundreds of years by transferring his mind from clone body to clone body. He has also produced a number of clone "brothers" (and at least one "sister") whose genes are based on his but have been tweaked to have an aptitude for something that will be useful to his long-term plans.
- A Memory Called Empire: Teixcalaanli law requires citizens to have a genome at least 10% unique for identification purposes, but the Emperor's heir is a "ninety percent clone".
- Project Nemesis: The titular kaiju Nemesis originated as a clone of the deceased Maigo Tilly that was infused with the genetic material of an alien monster. After Nemesis is nearly killed at the end of the second book, she expels a reconstituted Maigo who possesses superhuman abilities.
- Stardoc: Cherijo Grey Veil is not only an Opposite-Sex Clone of her "father" but was also modified with a Healing Factor that makes her virtually immortal.
- Vorkosigan Saga: This is Inverted with Miles's clone-brother Mark. As Mark was growing up, he was altered to match Miles's appearance, because otherwise he would have come out looking rather like their cousin Ivan.
- Pokémon. Mewtwo is a genetically modified clone of the mythical Mew, looking more humanoid and being stronger than it. At its introduction it was the strongest Pokemon of the game, and thanks to Mega Evolution contests that position with Mega Rayquaza. Unfortunately for its creators, Mewtwo proved too strong. In the manga, the Mew DNA sample was incomplete so the scientists spliced it with human DNA; in the animated movie (at least its Western dubs) they simply chose to make him stronger.
- Fate/Grand Order:
- Jeanne d'Arc Alter is the result of Gilles de Rais wishing for a Jeanne that's more inclined to his thoughts: a vengeful saint who wants to destroy France. Jeanne herself is so pure that she doesn't feel any grudge towards the country that betrayed her, so Gilles wished upon the Holy Grail for the next best thing: a "darker clone".
- Cu Chulainn Alter is the result of Queen Medb's wish of the Holy Grail for a Cu Chulainn that's closer to her fantasies - he's stronger (and looks more monstrous) and his personality is the complete opposite of Cu's.
- In the sequel to Destroy All Humans!, after Natalya is killed, Crypto uses the cloning machine to bring her back. However, he makes a few adjustments, which are for her to be head over heels in love with him.
- The main plot of M.U.G.E.N's fullgame Anti-Gouki Project is about clones of Akuma made with this fighter's DNA but implanted with different personalities and powers, being the game a Tournament Arc that decides which clone will lead the Clone Army to Take Over the World.
- Saints Row: The Third: The Syndicate's muscle mooks, the "Brutes", are heavily dumbed-down and hyper-weaponized clones of ex-KGB agent Oleg Kirrlov. His contribution to their development wasn't exactly voluntary, and after being liberated he helps the Saints bring down the Syndicate.
- In Genocide Man Fumiaki made some "improvements" to his clone-son Kenshiro's genome, better looks, no astigmatism, replacing his brain with an AI core.
- In The Petri Dish, Thaddeus Euphemism creates four clones of himself. One of them comes out shorter than the others and another has breasts because he used too much estrogen.
- In one episode of Family Guy, Stewie makes clones of himself and Brian and reduces their intelligence to ensure themselves superior. They also suffer a bad case of Clone Degeneration.
- In one episode of Kim Possible, Drakken decides to perform cloning for his next evil plan. Since Shego refuses to participate, he decides to make clones of Kim instead. In order to make sure the clones aren't heroic, he modifies them to have the reflexes of a king cobra, the strength of a rogue elephant, and the killer instinct of Commodore Puddles.