If anything, Sakurai is (as always) just limiting things needlessly because of his dumb worries about "individuality". It won't harm anything. The people who want Peach's voice and model will use the Peach costumes and the people who would want either Daisy or Rosalina would pick those. The same would apply with any other characters who had alt outfits. The same DOES apply to Wario's and now to the two Fit Trainers.
If anything, he should be seeing this as a way for him to completely avoid making complete clones while still putting in other characters that people like in a way that wouldn't bother them too much. Then again, Toon Link is proof that the whole "clone" thing isn't as much of an issue to him as he tried to make it seem.
I swear, that would never be an issue if all the clones were either just alternate costumes, or were built more like Luigi.