Yup, of course it wasn't smooth sailing for Waluigi as well. There were
rumors that a Mario brand committee were made in 2009 or so that curated how Mario content should look like to protect the brand. Funnily enough a few years after that committee was formed we saw a lot of changes, Toadsworth stopped having major appearances in games, Kremlings stopped appearing in Donkey Kong, Paper Mario got a massive hit in it's creative potential, and of course, Waluigi got cut from Mario Kart 7. If Waluigi wasn't popular within the fanbase and the backlash to him getting cut wasn't notable then he likely would've remained dead.
I don't know if the Wahoominati is real or not, but it would explain the weird changes within the Mario universe in the early 2010s. I'd love to say this group isn't relevant anymore, but we saw Origami King and Tanabe going on
record to say that it's not possible for Paper Mario to be creative like the early games. Now not all is gloom and doom, we saw with K. Rool getting in Smash that the Wahoominati doesn't have the same veto power when it comes to Smash and Sakurai has the last word. But sometimes I wonder if Waluigi not getting an important role in a game is due to executives vetoing it.
In a way Waluigi kind of reminds me of Boba Fett, he's popular with the fans but his owners don't like him. Fan support is what kept Waluigi alive all this time and it is what will keep him alive in the future.