Sakurai hasn't included that many references to non-canon games. Mario Party has no representation at all...and Mario Tennis has Waluigi. Wario
might have a move from Mario Strikers. Mario Kart has the best representation out of the Mario spinoffs, and it's probably because it's made by Nintendo themselves and not outsourced. Of course there's trophies here and there but nothing like a stage, or even an item.
I think I saw it mentioned in this thread, but when
Sakurai was asked about Daisy in Smash 64 he noted that she hadn't been in any games lately. Of course,
that's Smash 64, and since then she's made a comeback through the spinoff games and Sakurai did include a Daisy alt for her fans. I think Daisy is recognizable among general Nintendo fans --which is a plus. However, her lack of canon appearances severely hurts her. I think she might be in the same situation as Waluigi to be honest. Recognizable, relevant but lacks proper
source material. But Sakurai has surprised us before, so we never know.
As for the "Too many Mario characters" I don't think that's an issue. If Mario is a popular series, it deserves more representation. Plain and simple. Smash has never been a tit-for-tat series, it's about appeasing the most amount of fans. Of course you need other series here and there, but the majority of the cast are SUPER popular characters.