Toad - He's in already. Use Peach's standard special move.
Waluigi - Waluigi is only associated with Wario through the Mario spin-off titles. In WarioWare, Waluigi is NOWHERE to be found. A freaking arwing made it into WarioWare before Waluigi did. So no, that's not a good reason.
I agree that Paper Mario and Bowser Jr. take priority but the reasons you gave could have been several times better. And I hope you're not disappointed in Toon Link and Zero Suit Samus.
Mario's partners in the Paper Mario games were minor characters. They were merely there to assist Mario and that's it. Geno was a major character. Now, Mario's partners and Geno both have backgrounds and both fight alongside Mario but if you've played Mario RPG then you know that it was more like a team effort rather than switching out partners at random.
Bowser and Toadstool are both major characters and they aren't consider mere supporting characters. Geno and Mallow had just as much importance in that game as either of them. It's hard to really explain it but there is no way that Mario's partners in Paper Mario took priority over Geno. None of them impacted the overall story. Geno's background did.
Mallow & Geno as a tagteam are more than a match for any star character. Two major characters can compete with one star character. I can see Megaman getting in over him but not any other third parties. And Geno & Mallow appeared in a game alongside Mario so they're more Nintendo than Megaman is.
Daisy is only cannon through a minor role in Super Mario Land. And her role was severely minor in comparison to Geno's role. She's heavilly more important in spin-off titles. And if you're going to start drawing from spin-offs than that would mean Waluigi and Daisy would have to compete for a spot on the roster since they're both equal in terms of significance (which is slim to none).
Edit: I'm not speaking from fanboy-ism either. Take a minute and read what I'm saying before blowing off as fanboy-ism.