I was looking for your suggestions of what alt moves would be, and found nothing. I did, however, find this.
We actually get most of our Pokemon content from the anime. Sakurai has stated that when it comes to Pokemon, he has a different rubric of what he goes by for Pokemon inclusion at least as characters), and this includes heavily what is relevant in the movies and the anime.
We have seen that Mewtwo's representation as an antagonist was based on his movie counterpart. Lucario and his Aura abilities were first seen in the movie, and then in smash, as well as either character, or Jigglypuff, being in Super Smash brothers at all.