Team Rocket
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Team Rocket could be a cross between Pokémon Trainer and Ice Climbers. Jessie and James would be the Pokémon Trainers in the background. Meowth would be the Popo of the team. Ekans and Koffing would take turns as the Nana of the team via down special (down B).
Meowth would provide the normal moves with scratching, biting, and throwing coins. Ekans and Koffing would provide the special moves. Basically Team Rocket has one set of normal moves (Meowth) and two sets of special moves (Ekans and Koffing).
Meowth & Ekans team could have moves that involve paralyzing glares, constricting, swallowing and spitting up.
Meowth & Koffing team could have moves that involve explosions, poison clouds, and sludges.
Eevee
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Eevee evolves once per battle? How about per stock?
If an Eeveelution gets KOed, it comes back as Eevee and you can choose another Eeveelution.
Eevee’s standard special (neutral B) could be Eevee choosing between the evolution stones.
Everstone = Eevee doesn’t evolve but neutral B is now a Normal type move.
Water Stone = Eevee evolves into Vaporeon and neutral B is now a Water type move.
Thunder Stone = Eevee evolves into Jolteon and neutral B is now an Electric type move.
Fire Stone = Eevee evolves into Flareon and neutral B is now a Fire type move.