You know, there is nothing wrong with clones by principle, but the reason why people are bothered by Smash 4's is because they are blatantly worse versions of the original.
Dark Pit's only differences are that his Electroshock launches sideways rather than upwards (which can situationally be better than Pit's, but Pit's is better most of the time), his arrows do 1% more damage uncharged (2% more fully charged), but can barely be directed, and his F-Tilt does significantly less knockback. These are just blatant downgrades from Pit, and add absolutely nothing to him. He has no "niche". He would have been better off as an alt.
Lucina I've already gone into, and once again, I think she doesn't successfully fill her niche. Would have been better as an alt.
Dr. Mario, while having a substantial amount of changes and has one or two minor things that are better about him, only ends up as a much worse Mario. A Mario that only benefits from playing defensively. Mario, on the other hand, can do that BETTER than the Doctor, while also being very efficient at a whole lot more. He would have added more as an alt (for me personally, Mario is my third main, but I prefer Dr. Mario's aesthetics. I hate how Dr. Mario plays though, so I don't play as him. If he were an alt, I would get the best of both worlds).
No, it isn't a valid argument. They could have easily squeezed Alph in as a DLC clone if they just kept the other three clones as alts (since giving them any differences take more time than making them just alts, which was apparently a stage they were already at before making them clones). They could have even packaged him with Mewtwo in the Club Nintendo promotion, as a nice extra.