So are controls still up in the air?
I'm ambivalent about the screen-clearing super move idea, but I think manual smash hits would be a nice way to make the fighting a bit more fun.
In the NES original just had you tap the B button like crazy and after 3 to 5 punches that seemed to do nothing your toad would automatically do some flashy move that actually did damage. Fighting would be a lot more interesting if the player chose when to unleash the smash and there was some degree of trade-off as to how many light punches you threw before unleashing the big hit, perhaps softening them up more first results in more damage per hit, but too many hits and the enemy will stop being stunned and hit back, along with the time you take giving other enemies a chance to cut in.
As for the input, aside from mapping smash hits to a different button, you could hold the button a moment to charge the hit. (There was usually a pause before the smash hit, so it could be in that rhythm.) This would also allow players to pick out what smash hit to use by pressing a direction while releasing the attack button. (Or there's direction + attack at the same time, but that seems like it would be too easy to accidentally trigger.)
Of course the running attack should be same as it ever was.