My guess is that as costumes, characters like Dr. Mario would share statistics in the Fighter Records with Mario. He couldn't figure out a way to separate the statistics properly, so split them off. Same with the others, obviously. I can agree with this. Maybe next game he can put them on one slot properly by using an L/R switch method.
Maybe. Perhaps the data structure of the game wasn't made with variations in mind, so the only way to record those fighters' records would be to split them off, even if the changes were minimal.
But I feel that Sakurai wants costumes to be merely aesthetic changes in the sense that, if you change a costume via X/Y buttons, you won't be altering the gameplay at all, whereas by selecting a different roster slot, there will be changes in gameplay. There's some real consistency here.
Maybe Alph was also considered to be separate but they didn't come up with any ideas to make him different from Olimar that would be easy to implement. I mean, there are the Rock Pikmin, but maybe they thought they would be too similar to Purple Pikmin, not to mention he wouldn't always have those Pikmin at his disposal, so the differences would be minimal, even more than Dark Pit's differences compared to Pit. Another idea would be to replace the Hocotate Ship with the SS Drake (different hit boxes for the Final Smash), but the latter already appears in the background of the Garden of Hope stage, so it's not a feasible option. Lastly, the Japanese version calls them "Pikmin & Olimar/Alph", implying the main focus are the Pikmin, rather than the captains, so it might also have been a factor to not make Alph a clone. There's also the fact that Alph doesn't have the same level of popularity as Lucina and Dark Pit have, at least in Japan, so it's a valid reason to leave him as a lower priority for the clones, assuming they also considered on turning him into a clone but ran out of time.
Other possibilities would have been the gender swaps, Wario's costumes or Mac's costumes, but they're identified as the same characters, so it would be absurd to separate them. The Koopalings are only other characters that could have been clones, but given there are 7 of them, it would have been overkill to separate them all, not to mention how they would have to try and make each Koopaling as unique as possible. Partially separating them would be odd.
Removing Marth's tippers was an easy addition, as those are a slight change on the hit boxes. It's an easy way to make a newcomer-friendly version of a character. Lucina was thus separated.
Dr. Mario had slight changes to his moves, which are simple value changes, either knockback, damage, hit boxes and even the elemental effects. Dr. Tornado and the down air are based on Luigi's given the similar models, animations and move proprieties.
Dark Pit had slight changes to some of his moves, so once again, basic value changes. The Final Smash is based on Zelda's and was likely implemented because they had Zelda's Light Arrow as a basis to make another powerful straight-line projectile attack.
The common denominator is that all those ideas and changes were easy and fast to implement and were free of potential issues as they're based on finished content. Given they're essentially copy-pasted content, the probability to run into bugs was quite low. They wouldn't have been added if they were bigger trouble than worth.