A clone is a character with a moveset and physics that are considerably similar to another character's. Often, the clone's moveset will have a few tweaks made, and may have their physics altered to a degree, but on the whole the characters are similar and typically have the same special move mechanics, to such a degree that both characters can be played optimally using a very similar or even identical play style. Clones are a common inclusion in various fighting games, as developing a character using an existing one's moveset and/or model as a base is less time- and resource-consuming than starting from scratch.
Semi-clone is a term used for characters who share some of their moveset with another character, with some similarity in physics, but have enough differentiating moves and characteristics that calling them a "clone" wouldn't be entirely accurate. "Semi-clone" status can differ among player's minds depending on their basis of the term; for example, one basis for dubbing a character a semi-clone would be their differences in Special moves from whichever character they are clones from. This process of a clone breaking away from its roots and establishing its own identity as it divergently evolves is known in the Smash community as Luigification, named after how Luigi originally was a clone of Mario but eventually came into his own in both the Super Mario and Smash Bros. series. Jigglypuff is the only character who started as a semi-clone and eventually became its own completely unique character.
Super Smash Bros. 4 introduces alternate characters that act as alternate costumes, namely Alph for Olimar and the Koopalings for Bowser Jr. They have their own voice clips and the Announcer refers to them by name. However, since they bear no gameplay differences and are not treated as separate characters, they are not considered to be clones.
The term "clone" is also used to refer to individual moves cloned from another character's move. For example, Falco's Blaster is a cloned move of Fox's Blaster, with the former being the same general type of attack with animations taken from the latter, but with altered properties and functioning so that makes it its own move. Usually cloned moves share animations, while altering the cloned move's function and/or properties in some way, though sometimes the inverse happens, such as in the case of Ness' and Lucas' down tilts; Ness' down tilt is a low rapid kick where he pokes his foot out, while Lucas' involves him rapidly spinning around while kicking, but both have identical functioning as extremely fast but extremely weak low kicks that semi-spike with a high tripping chance. Cloned moves can also happen between characters who otherwise have no other aspects cloned, such as Charizard's Flamethrower being cloned from Bowser's Fire Breath, both being the same type of move with identical animations and functioning, but with a minute property difference (Charizard's Flame Thrower reaches farther with thinner hitboxes in Brawl, and in Smash 4 it flinches with all its hitboxes while Bowser's doesn't alongside his covering a larger area).
Clones in Super Smash Bros.
Smash 64 only had one clone in Luigi, and a semi-clone in Jigglypuff, with the rest of its cast consisting of unique characters. All of the unlockable characters were created with the premise of reusing some of the pre-existing characters' movements and models.
Clones in Super Smash Bros. Melee
Originally, Masahiro Sakurai was going to include significantly fewer playable characters in Melee. However, with fans wanting more characters while time was constrictive, Sakurai decided to add clones later in development to pad out the roster, as these characters would take a lot less time to develop than unique characters. This led to Dr. Mario, Pichu, Young Link, Falco, Roy, and Ganondorf being added to the cast as clones. Luigi and Jigglypuff also returned, though Luigi was significantly decloned into a semi-clone, and Jigglypuff was decloned to the point of not even being a semi-clone anymore.
Clones in Super Smash Bros. Brawl
Among the Melee clones, four were completely cut from the roster (Pichu, Young Link, Dr. Mario, and Roy). The two clones that returned, Falco and Ganondorf, were significantly decloned to being semi-clones. Luigi was also slightly decloned further, though mostly through Mario being given new attacks. Among the 18 new playable characters, none are complete clones, with Toon Link and Lucas being semi-clones. Wolf takes a couple aspects from Fox.
Clones in Super Smash Bros. 4
Super Smash Bros. 4 reintroduces true clones, adding two new clones, Lucina and Dark Pit, and one returning clone from Melee, Dr. Mario. These clones, unlike the Melee clones, were originally developed as alternate costumes of the characters they were cloned from, similar to Alph and the Koopalings. Later in development, they were given moveset alterations from their originals - according to Sakurai, Dr. Mario had to have the differences from Mario he had in Melee in order to avoid disappointing fans of his previous appearance, Lucina was given no tippers to act as an easier-to-play version of Marth, and Dark Pit was given a different Final Smash, as Sakurai did not like the idea of him using the Three Sacred Treasures. Once these changes were made, however, it was decided that they each would be promoted to full characters, as "even a small difference in abilities" requires a unique roster slot. SSB4 groups these clones in their own area together on the character select screen, rather than placing them with their respective franchises.
None of the newcomers are semi-clones. Luigi, Falco, Toon Link, and Ganondorf remain as semi-clones, though they were only minimally decloned. Wolf, whose moveset partially derived from Fox, was cut from the roster, while Lucas and Roy return as DLC. Roy is now a semi-clone, as his moveset is further distinguished from Marth's.
Most clones and semi-clones also share at least one custom move, though true clones (Dr. Mario, Lucina, Dark Pit) have more custom moves in common.
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