Well Daisy actually has more merit than Waluigi.
She has a baby which only she, Mario, Luigi, Peach, DK, Bowser, Wario and Yoshi have. Irrelevant.
She has been in every Mario Party except for the Game Boy since her debut in it. Same with Waluigi; he was even brought into the Party series at the same time as her.
Since Mario Kart Double Dash, she has been in every Mario Kart game to date, which all of the other secondary characters did not make it in (besides minions, Rosalina, Honey Bee and Metal Mario.) That's supposed to mean something? She's an easy model edit.
She has appeared in every single sport game since her debut. Same with Waluigi. Hell, he's been in Mario Tennis Power Tour while Daisy and even WARIO were not.
She has been in Melee and Brawl as Peach's alternate costume so either Sakauri notices that she exists or that she'll easily be a clone. Again, with her stark similarities to Peach, being an alternate coloring for her is easy to see. It's not like Sakurai doesn't ignore Waluigi, though. He refers to Waluigi as a positive thing for Luigi in Luigi's Melee trophy, and states he has has "many brilliant game appearances" in Waluigi's Brawl trophy. And again, WHO is an Assist?