On 3DS: make Select to be the taunt button (select+the directon on the D-pad or circle pad forthe different taunts) and use the D-pad for walking and tilting, and make X a dedicated short-jump button and Y a dedicated full-jump button. This would solve all the problems the 3DS has on the controls without removing anything relevant.
A revamped Pokemon trainer (new mechanic: Power Points. The specials have limited uses, and get restored by changing pokemon) with Sceptile (a mega man style zoning fighter)+Charizard+Greninja.
The idea is: vs fast fighters, Sceptile tries to zone them, while vs slow fighters, Greninja can freely combo them. Charizard's stronger and armored attacks are perfect to finish off heavily damaged opponents and break into enemy zoning caracthers.
Also, make the Down Taunt have some remote use for all caracthers, to add some layer of strategy. For example,for PT, Sheik or Samus, it changes forms.