User blog comment:Legendary Pop-Fizz/Make a clone/@comment-6684591-20150414102019/@comment-5185663-20150414174725

''There are 3 fighters [Lucina, Dark Pit, and Doctor Mario] that are alternate models (clones) in the game. Each was originally a color variation, but during development, they were given balanced characteristics. Since their functionality had differences, forms were separated from each other. However, it was vital that this didn’t increase the required man-hours. Some relative tuning was sufficient as it wasn’t necessary to create balancing from scratch.'' ~ Masahiro Sakurai

What happens is the variant version of the existing character is given a different file as its own fighter, and small tweaks that take less man-hours to get done make them new.