I don't think you can really hold the SMB2/USA situation over Toad's head though, because honestly the same could have been said of Peach at the time of that game. I do agree though that having two Toads in the NSMB games isn't really necessary, I think Nintendo should have replaced Yellow Toad with Wario and called it a day just to diversify the line up. Aside from that though, I do think Toad definitely deserves his spot in the recent Mario games, heck 3D World feels like a callback to SMB2 so it would actually feel wrong for Toad not to be in the lineup for consistency's sake.
I don't have a problem with either Wario or Rosalina because the former is the star of his own series of games and has a unique gameplay style, while the latter has played a significant role in what is considered by some to be the best Mario game ever created. (and by that logic Rosalina is an even greater "helper" character than Toad that has yet to have any significant role in Mario games aside from helper character)
I would hate Daisy or Waluigi getting playable spots in Mario series games / Smash Bros. Both of those characters are the epitome of "ugh" and bottom of the barrel Mario characters just hauled out to expand the playable roster of spin-offs. Daisy's role in the main series is a thank you / game over screen in SML, hardly deserving over Toad. Waluigi doesn't even have that, the main reason why people like him is exactly because of how lame he really is. I'm actually surprised Sakurai bothered to acknowledge him as an assist trophy in Brawl.
I think one big thing you are missing however, is that Toad has his own unique identity and design that separates him from a lot of those other characters. For instance, the other plumbers in the series are heavily based off of Mario's design, the same goes for the other princess' being inspired by Peach, as well as the Koopalings/Bowser Jr. being based off of Bowser's.
I do not think has any unique Idenity, that is the problem. He is Nurse joy, I don't care about him.
However I you feel as though he is important, that is fine. You see an importance that i do not really think exists.
I disagree.