I would finally give Bowser and Ganondorf their own stages.
Bowser's Castle would be modeled after the one from New Super Mario Bros Wii, but a different art style, and there would be functions of the other of Bowser's Castles. I'll do the lava hazards, there'll be an ax that breaks a bridge, cannons that shoot fire from the Mario 64 Bowser levels, and a big buddha-like statue of Bowser in the background.
Ganondorf's level will be modeled mostly after the Ocarina of Time finale. Not too much unlike the design of Ganon's boss fight from Ultimate, but smaller and bringing some of the broken architecture towards the front of the battlefield for the sake of convenience. The gimmick would be a Master Sword stuck in the ground that once touched, an OoT version of Zelda would come in and use her Seventh Sage power to fire that beam of light and freeze someone in their place, and only a smash attack could get them out.