Yoshi's Story for the N64 didn't have Mario in it, as far as I can recall. I'm curious, though, who's the sixth Mario rep? I thought it was five, Mario, Luigi, Bowser, Peach, and Rosalina. Unless you were counting Yoshi, he's technically his own series as far as Smash is concerned.
I don't think that devalues your argument, though, 6 Pokemon and 6 LoZ characters is legit to me.
Also, I just noticed a thing regarding Dark Pit. (@
MorbidAltruism you might like to see this) (Also, you're all welcome for bringing this up again)
If you look through the illustrations for newcomers on the main website, there's only two characters who aren't confirmed playable on any of them. For Robin's, you have Chrom, but we already know he's a part of Robin's Final Smash. In the background of Palutena's, you can see Dark Pit flying in the distance. We already know he's not part of either Pit's or Palutena's final smash, so that, to me, implies he will be in the game in some form at least, and points even more to his inclusion as a clone/avatar.