In my long, long list of grievances against Nintendo, this is one that places somewhere in my top five.
It all goes back to these two gentlemen:
Shigeru Miyamoto and Takashi Tezuka are two of Nintendo's longest serving employees, and they are the two most directly responsible for the Super Mario series, being involved in nearly every major release (the exceptions being the two Super Mario Land games). They've long been the show runner and co-show runner of the Mario series. The problem is, at some point the Mario series either got too big for them to keep track of the events and characters from every game or they willfully lessened their involvement with some of the branch titles such as the RPG series and the sports game.
Point being, Miyamoto and Tezuka don't give really a rats ass about Waluigi as they had little to nothing to do with his creation, even less so the Wario Ware characters (Wario Ware is more of a Yoshio Sakamoto thing).
Now, stop and think for a moment about when the last time you saw Wario in a main series, platformer Mario game. When did you see him acknowledged as being part of the series universe in a 2D or 3D Miyamoto or Tezuka-led Mario game (Super Mario 64 DS being the exception that proves the rule)? You didn't! Its not that Miyamoto dislikes Wario (actually, he might), its just that he seems to have in mind the same simple, "Mario Luigi Toads Peach Bowser" game universe that he and Tezuka designed 28 years ago, and, either out of ignorance or stubbornness, refuses to let any of the world-building that's been taking place in the branch Mario titles seep its way into the main Mario titles.
Until a Mario game can be made without any of the Super Mario Bros. old guard involved Princess Daisy will not even cameo in a main series title, Ashley will not be the haunted mansion boss that Mario fights, 9-Volt won't be in any Smash Bros. games (he is from a "lesser" game in the Mario universe, after all), and Waluigi won't be Luigi's surprise nemesis at the end of a Luigi's Mansion game.
TL;DR, The fact that some Mario and related series games are considered B-tier while the platformers almost invariably are considered A-tier and characters from the B-tier Mario games never cross over into the A-tier is incredibly stupid, and I blame Miyamoto and Tezuka. Having Wario and Waluigi pop up as villains in a NSMB game would be a lot less lame than Bowser Jr., at least.
*Says some unflattering things about Miyamoto and Tezuka, braces self for inevitable backlash*
How about they make a new character for once.