Commanding Pokemon

Basically, when a Pokémon’s Initiative in combat comes up, simply let the player decide what the Pokémon does. You do not need to announce your Pokémon’s action during your Trainer Turn.
Pokémon can do the following with a Standard Action:
» Use a Move or Struggle Attack
» Use Combat Maneuvers
» Activate an effect that requires a Shift Action. This cannot be used for Movement.
» Use Abilities, Capabilities, or make SKILL Checks requiring Standard Actions
» Recall themselves into a Poké Ball for a Switch
» Pick up Held Items
Additionally, Pokémon may drop most Held Items using a Shift Action, though this varies.

Note: The topic of “uncommanded” Pokémon in general is a bit tricky. As a GM, you shouldn’t be too strict about only “commanding” one Pokémon at a time; it’d be ridiculous that a trainer couldn’t go on a walk with all of his Pokémon because “only one can shift at a time.” The point is to not let Trainers have an unfair advantage in battle. Feel free to control “uncommanded” Pokémon in any way you choose to achieve this goal and to just make sense.
You may also create special Double or Triple Battle League events where can Trainers command two or three Pokémon at a time within those events without the need for FEATURES  such as Focused Command. Another place where you may wish to bend the rules when it comes to number of Pokémon turns a round is how many Pokémon a villain or other NPC can command at a time. Remember that the limit is there for the sake of balance on the PC side. If your encounter balance requires a villain to have multiple Pokémon on the field at once, then go for it!