I don't have a problem with Junior being in the Clown Car. I think it's very much worth noting that the Clown Car and the Paintbrush can coexist from recent media like Super Nintendo World and Bowser's Fury.
I think Junior should be allowed to evolve; the Clown Car was all he had in the times of Smash 4 and it basically eclipsed the paintbrush in its entirety, but now now that he uses both I don't see why the Paintbrush can't be incorporated in a more significant way. I'm not asking for the Clown Car to be axed entirely, I want him to wield the Paintbrush too.
What would the Koopalings wield? Their wands? I guess it could work. The main problem I have with them is that they look very weird since they have to be shrunk down to fit the Car. And like it or not, they
do homogenize Junior and themselves because they all share a set of same generic animations. There's no way the dev team didn't make Jr's animations without the other SEVEN characters they had to account for in mind.
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I guess you can solve these problems by giving the Koopalings unique taunt animations (which has a precedent since alts can have different cosmetic animations as proved with Byleth), victory screens, and really working with body morphing/visual trickery to make them fit in the car but grow into their actual sizes when they're outside of it. The Stoopid Unikorn's suggestion of having them use the wands for the Final Smash also works.
These would solve basically all the issues I have with this character at the moment. I'm questioning if it's worth all that extra work to keep the Koopalings around, but if people like them that much then Nintendo definitely has the resources to make them feel like not afterthoughts. If they're really going to go for this concept, then they should go all the way.