Dark Pit over Waluigi... and K. Rool, Ridley, Black Shadow, Medeus and Ghirahim just to name a few. They would have all been cool to see rather than an edgy Pit clone. Giving Ganondorf his own true move set would have also been great, but that takes too much work.
Also, inb4 how I am mad while my avatar says "Deal with it" and irrelevant arguments about size. For the record, I am very content with the game so far and it is not like Ganon is my main anyway.