Chikorita
Chikorita will use Razor Leaf as in Super Smash Bros. Melee.
Deoxys
Deoxys's act is similar to the one of Ho-oh in Super Smash Bros. Melee. It will float over the stage and unleash a powerful Hyper Beam (instead of Ho-oh's Sacred Fire.)
Goldeen
Goldeen is the only Pokémon you don't want to have released from your Pokéball. It's the most useless Pokémon of all (in this series) because it only uses Splash attack, which has no effect on any characters.
Groudon
Groudon stands on the stage and burns anyone who touches it.
Kyogre
Munchlax
When Munchlax appears on the stage, it will slowly walk around, eating any item it encounters on the stage.
Piplup
Piplup uses a Surf move to wash away competitors on the stage.
Snorlax
Snorlax will again fall from the sky and crush competitors as he did in Super Smash Bros. Melee.
Torchic