Ahh....but you are missing an entire spectrum of Pokemon representation...assist trophies!
"What? Pokemon go in Pokeballs you n00b!" Well, we could always have characters from the games guest star as ATs. Allow me a few examples...
Sabrina (Saffron Gym Leader) - Uses psychic powers to twirl all opponents in circles.
Giovanni (Viridian Gym Leader/Team Rocket Leader) - sends Team Rocket members out to use their Pokemon on you. They are mostly a horde or Rattata and Ekans.
Solana/Lunick (Pokemon Rangers) - Lasso opponents with their stylers, holding them within a limited area.
Pokemon Center Nurse - heals a certain percent of all characters health.
I wouldn't be surprised if some people from Pokemon games showed up as ATs. After all, Sakurai decided to use Pokemon Trainer as a character...I'm sure he'll bring some friends.