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when you start a battle there's an array of the 6 pokemon which will be available to you. these will be by default your favorites, as long as they have 100% HP. Otherwise they'll be the ones with highest CP at 100% HP. you can change any one of them by tapping it and choosing another, before you start the battle (GO)
hamster
@HatBeard
@>>>>>> are you switching pokemon when you fight multiple enemies in a gym? a small arrow icon appears during the fight that lets you change which pokemon you are using during a fight. useful if you get a mismatch and your attacks end up being 'not very effective'
not sure how it picks the pokemons available, either cp or from your favourites would be my guess. try favouriting your strongest ones and see if it offers you more than one to fight with next time.