Not sure about Pichu but all those characters listed had their own game or were the main characters for a game/series which isn't the case with Waluigi.
At least with Ridley, Sakurai gave an excuse even if it turned out to be flimsy in the end for his omission until now. With Geno, speculation usually revolves around Square owning the rights to the character for his omission.
With Waluigi, Nintendo can't even be bothered to make any excuse for his omission. They currently see him as nothing more than Assist Trophy worthy for the Smash series.
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