Turning Dark Samus into a clone would mean all work gone into making her an Assist Trophy go down the gutter. Wasting resources is hardly a good decision.
As for Dixie, @
Verde Coeden Scalesworth
and @
Naoshi
have already elaborated on it. Her model has significant differences from Diddy Kong to work as a clone.
They based the clones on already existing characters with already existing models and animations. Considering this, the only choices for clones in this game were Dr. Mario, Dark Pit, Lucina, Alph and the 7 Koopalings.
That means only other choice remaining would be Alph, who isn't a really popular character, even within the Pikmin fanbase, as far as I know. Besides, altering the Pikmin mechanics could mean more work than converting Dr. Mario, Dark Pit and Lucina from alts to clones. In other words, a risky decision that could compromise the project's integrity. Sakurai explicitly told that they didn't want to spend many resources and man-power on the clones in order to avoid balancing issues.
As for the 7 Koopalings, 7 Bowser Jr. clones would hardly be any good idea. And it wouldn't make sense to separate part of the crew either.
That leaves Dr. Mario, Dark Pit and Lucina. It was them as alts or them as last minute clones. Take your pick.