You still have a decent amount of control over your team even on auto. The major variable that people are unaware of is the importance of the order you place ninja into your team. Killer Bee for example, will always use his first mystery on whoever is placed into the team FIRST (Always will be your main unless you pick the main up and place him back down).
Another example is if you want a certain ninja to go r1, the person who is placed into the team LAST will have priority.