I don't know why Princess Daisy was absent in the SNES era and I'm not going to pretend to know why either.
However, if you compare Daisy's introduction on a portable gaming system in 1989 vs Waluigi's introduction on the N64 in 2000 the contexts of the circumstances are completely different. Waluigi was created by Camelot to be Wario's partner in Mario Tennis. Daisy AND Wario were created by Nintendo SPD since they didn't want to use characters that weren't their own. The purpose and image behind the character directly influences their relevancy and importance to the game its in. I'd say the very fact that Daisy first appeared in a Nintendo-made game as an important plot device (albeit, a substitution, but still there) gives her more prestige and importance over Waluigi. The only time Waluigi had SOMETHING over a plot in a Mario game (not even mainline) was DDR Mario Mix where he was a faux-villain to the actual villain of the game, Bowser.
There's no other argument for Waluigi's supposed "relevancy" over Daisy other than the very weak "but she didn't appear in other games for a long time!"
So?
And besides, I don't understand why this a legit criticism anyway. Relevancy doesn't influence my liking over the character. Seems like people are just obsessed with image and popularity.
Captain Syrup is more of a Warupichi than Mona is because she actually follows similar character principles to Peach (being a mirror to Wario) while succeeding in being a good polar opposite to her (a darker beauty, more active than passive, greedy, selfish, harmful to the protagonist, ect)
Mona is more like "Wario's friend/love interest" than anything. Not really similar to Peach at all. Plus the Wario Land games are an adventure style like the Super Mario series. WarioWare is a completely different series.