In an interview with Super Smash Bros. producer Masahiro Sakurai, he outlined reasons for including clones.
In the newest releases for Nintendo 3DS and Wii U, despite having an expansive roster, there are characters in the game that have "clone" characteristics - Ganondorf, Lucina and Doctor Mario as prime examples. Some, however, received different costumes over a single character slot - like Bowser Jr and the Koopalings.
Sakurai noted how that "any character which gained some uniqueness through their balancing needed to be separated so their results and statistics could be counted properly," using Lucina as an example. In addition, "what was needed for each of these changes was to reduce the work required to balance the game," he admitted.
When it came to Marth and Lucina, these characters "would only be tested against each other, until they were roughly equal and in balance."
What do you think of Nintendo and Sakurai's approach to clone characters in Super Smash Bros.?