I'm glad they're including alternate skins for some characters, since this might mean lessening on at least a few clones. For example, while I know he was only in Melee, did we seriously need Dr. Mario in that game? This time around, Dr. Mario can just be a costume. A few others I can think of:

Luigi = Mr. L
Peach = Daisy (yeah I know they already did something kinda like this in previous games with the yellow dress and slightly darker skin tone, but they could also change the voice clips and the face a little more)
Best I've got for the Pokemon characters is to just include their shiny version in addition to other stanard alt colors
Samus = Fusion Suit (since Dark Samus is an assist)
Olimar = Maybe Alph from Pikmin 3?
Toon Link = Young Link from Ocarina of Time and Majora's Mask
And in the same vein, adult Link could have a Fierce Deity skin (yeah this Link is based on a combination of the Skyward Sword and Twilight Princess designs, but I don't think it really matters, Mac has his wireframe despite not actually looking like the Mac from the arcade game)

This and being able to chose the gender of the Wii Fit Trainer now is leading the way for special disguise especulation.

Some of my favorite ideas I've seen are, Female Villager, Dry Bowser, Dr. Mario, Classic Sonic, Galacta Knight and Mr. L.