More so than Melee, these clones are bonus content. They've always been that since they were planned as alt costumes.
They just happened to have some spare time to give them their own slots. We have no idea what went behind the scenes, but we know that these three characters



didn't take so much time to make. It was them as alts or them as alternate versions of existing characters.
Like I stated in the previous page, if you're going to complain about them, you may as well complain about easter eggs or other bonus content that doesn't add to a game.
Developers doing stuff on their breaks isn't unheard of, especially if they're passionate enough about their work. A lot of the work was done on the clone trio when they were alts. They already had animated models, textures, voice clips and so on. All they did was to change a few moves and proprieties, something that all characters went through during balancing and testing.
Given the changes would cause statistical flukes on the records, they were given their own slots to separate their data. It might have to do with how the game's data structure is organized.
Dr. Mario was given the Tornado and the down air. Mario in 64 and Melee had them and Luigi has similar moves in this game. Nothing exactly new here. Worth noting is that Mario still has the Mario Tornado as his down aerial.
Dark Pit had the Upperdash Arm replaced with the Electroshock Arm. A model change isn't a big deal. His Final Smash is functionally based on Zelda's, so like Dr. Mario, they reused assets from another character.
Lucina is Marth without a tipper. Nothing major here either.
None of the changes required extensive planning and were made in much lesser time. These ideas likely arose when they were designing, balancing and programming Mario, Pit and Marth. Perhaps they felt leaving the characters as costumes wouldn't do enough justice to them?