Dr. Mario was planned as a costume, but he decided to do it for his fans. And his fans definitely loved him back as his own playable character with the Tornado.
Dark Pit was a last minute move. I do definitely believe there's some Sakurai bias going on for Uprising, not to a ridiculous degree as some suggest, but just a bit. But his team also worked on Uprising, so they could easily port them over and remake their movements/attacks for Smash easier than others. If you designed a character, you'd be best at porting them over. So I can honestly say it was a fairly logical move to put in the most content as easily as possible.(I think more series should've been repped a bit higher, respectively, but eh. Not even mad, truthfully)
Keep in mind that it was Dark Pit or Alph. He has to make the Rock Pikmin work, which he might've not thought they would be any different from the Purple Ones. So, making him unique might've been something that couldn't come to mind at all. Dark Pit has a somewhat different special moveset(uses different items, although clonish versions) and his Dark Pit Staff, a major item he uses in Uprising. Despite his low differences, they are notable enough to be a change. The last bits of Alts were all 7 Koopalings. ...7 last minute clones is pushing it. The one issue that seems to happen is that some people cite Dark Pit to have a different weigh/knockback/recovery ability/etc., while others say besides 2 specials(customs too, technically) and Final Smash, he's identical. Also, they have different armbands and as metal, their wing textures are separated. They're much easier to tell apart than some feared would be a minor issue.(The Wii U version doesn't allow you to select a box over a character in battle to help show which person is playing from what I remember. I think he didn't bother to do that, but I would be okay with that too as an option)
Lucina was explained very well. She was a different style of Marth, without the tipper, shorter and naturally has less reach. Their approaches are very different due to this. Their entire moveset is identical for anything that affects battle. Her taunts/voice/victory screen are different, of course.
It should go without saying that many character Entrances are unique, clones or otherwise. In fact, I think the only ones with an identical entrance just happen to not be clone at all, ironically.