well one way i see how you can manipulate what/who/which ninja in your line up do at each turn is by checking how much the chakra for the mystery is, is it prompt or not, and how to combine ninja that give chakra each turn and ninja that have lower cooldown on mystery so they can cast it early on.

in short, the effect you desire for that particular team aka the 'Theme of that Team'
example : mass clone team - status team - the works