All interesting ideas.

I think they would keep the glass dome, however, because without it, the different shapes of Jr. and the Koopalings might affect the hit-boxes (or perceived hit-boxes, at least).
On a side note, imagine this:
A newcomer trailer set in Mushroom Kingdom U. The Koopa Clown Car flies onto the scene, perhaps coming to the aid of Bowser, who has kidnapped Peach and is fighting Mario. Cue montage of game footage showing the Koopa Clown Car punching with its boxing gloves, bouncing on its propeller, firing Bullet Bills, lobbing Bob-ombs and Mecha-Koopas, dropping Big Steelies and more, all while the pilots change inside its glass bubble.
Then...
Something shoots the Koopa Clown Car out of the sky! A pixelated bullet smacks into it and sends it spiraling into the familiar Mario bushes. And from out of the bushes appears the Duck Hunt Dog, laughing with its paws to its mouth. Cue the game footage of the Duck Hunt Dog doing his thing, wielding the NES Light Zapper and working in tandem with the ducks themselves.
It'd be a hell of a trailer and add some much-needed visual variety to the roster (animal characters, colors other than blue, etc).