If they put Miis in Zelda or Metroid I would agree with that argument, but this is Mario. The story is irrelevant.
The story of the Mario games may be irrelevent, but the atmosphere of those games is not. And that's what would stand to be destroyed if Miis were introduced.
Miis are an invasive species. When you introduce them into an ecosystem which can't handle them they tend to destroy the native species. Its what what happened to Australia after rabbits and then foxes were introduced. These things don't belong in Australia, and many native species have become extinct as a result of their presence. The same would go with Miis in any game they would invade. Mario and the mainline characters would be safe regardless, but the presence of Miis might push out some of the more minor characters like Toad, Birdo, Shyguy etc. These characters might otherwise have been in the game, but if Miis are there it might have tipped the balance and developers might not bother.