Mentioning Final Smashes, taunts, and victory animations won't sway my thoughts on clones. I know Dr. Mario is more like Luigi, but I still think could have been a palette. Compared to the three clones, I'm not too upset about Dr. Mario. I think if they kept Pit's movesets from Brawl and gave what Dark Pit has right now in this game, I would have been fine with the addition. Sure, they would have many of the same attacks, but there would be that more noticeable difference. I certainly can't change the game since it's what it is now, and I'm content with the roster as is. I just think they could have done things a bit differently is all.
They're last minute clones, added as little extra when the development team was already wrapping things up. They took nothing from the game's quality nor did bring anything new. They're just that: bonus content. Nothing more, nothing less.
Dr. Mario, Lucina and Dark Pit were just alts not unlike the Koopalings, Alph or female/male variants of Robin and Wii Fit Trainer.
I think Lucina is fine. She was one of the protagonists of Awakening, was highly popular, and FE getting four characters isn't that crazy. She makes sense as her own character, and as a clone of Marth.
Dark Pit being his own character above Alph though is just silliness. Alph was the protagonist, was more than just a glorified colour swap, and Pikmin getting two characters makes a whole lot more sense than KI getting three, let's be honest.
I don't think the development team is nearly as concerned as this fanbase in regards to "reps" and characters per series.
They do what they can work with and into. Having Alph use Rock Pikmin, for example, would require more work and resources than Dark Pit that barely took any and was shoehorned as a clone at the very end of the game's development cycle, even after the other two clones, which is why he has barely any changes from Pit and the only thing that sets him apart from his counterpart is a Final Smash that is copy-pasted from Zelda's, right down to the move's proprieties (damage, knockback, ...).
It's all very beautiful talking about "series reps" and "series justice". Those mean jack squat when it regards limitations in budget and workload.
But really, this is beating a rotting carcass. People still are ignorant about game development, whereas I have researched on the subject and dabble in computer programming regularly. I'm not trying to sound arrogant here, but it's far easier for me to understand Sakurai's logic when I myself have experienced what he has, even though at a much smaller scale, but it's not like I can't extrapolate my experience to different realities.
The game is as it is now, there's the possibility of DLC with Mewtwo around. Those three clones have an insignificant impact in the game as a whole, both in content and its production. It's time people moved on from this. The solution is simple: don't like the clones, don't play them.
The "wasted slots" logic went down the gutter now that the development team can add more characters to the roster if they want to and, of course, has the resources to do that. What's done is done, you can't change the game, but you can look for the future.