About Shulk, Ryu and others newcomers, what matter is that most of the alt colors are references.
Obviously, there's the Koopalings, but Little Mac is full of references too, and the villagers as well. This also applies to veterans' new costumes, like Link's SS and Oni costumes, ZSS' shorts, or Metaknight's Galacta and Dark colors.
Of course we have exceptions, such as Dark Pit colors.
But no matter what, I think it's sure that we will get references of some sorts. In SSB4, there's no need to always have blue, red AND green colors anymore.