There are a bunch of consistant rules on how the autobattle AI uses skills. First of all, position/initiative doesn't seem to matter at all. What matters is the chakra cost of the mystery, the order the ninjas were placed/moved, and some special conditions like interrupt/heal skills. The order the ninjas are placed is changed whenever you add a ninja or move a ninja. Adding or moving a ninja puts them at the end of the order. So for example, if you add Naruto, Sasuke, and Sakura to your team in that order, you ninja order will be Main -> Naruto -> Sasuke ->Sakura. If you then move Naruto to another spot (or move him and then move him back if you want to change your order but keep the same formation), your new order will be Main -> Sasuke ->Sakura -> Naruto. This order is also the order the ninjas will do their start of combat effects, like clones and shields/buffs, which is important if youre trying to get certain clone setups or have shields hit clones.
Mysteries get cast by the AI using this priority:
1. Chakra cost (high -> low)
2. If skills with the same chakra cost can be used, they will be used in reverse ninja order
These are the general rules for most mysteries. Interrupt mysteries behave differently. It will save chakra for them initially (didn't do enough testing to figure out exactly how long it'll wait, but it seems to usually be around when move 2 starts/ends) and use them at the highest priority if the enemy uses a skill. Otherwise they will be used at the lowest priority. So roughly:
0. Interrupt skill (if the enemy is using a mystery)
1. Chakra cost (high -> low)
2. If skills with the same chakra cost can be used, they will be used in reverse ninja order
3. Interrupt skill (if the enemy is not using a mystery)
Support skills (heals, revives, etc.) will be cast when they will do something (not sure on priority). This is a pretty general description of how they work, but it's enough for most lineups that just want mysteries cast in a certain order.
If you post your team and say what you're trying to accomplish mystery-wise, I can probably figure out how to make that happen. If it's just having your pos 1 cast it's mystery instead of your pos 4, just move your pos 1 to another space and move it back (to put it at the end of the ninja order).
EDIT: Also want to echo the above comments that there are a lot of small nuances that may cause skill to go off not in this order, this was just a very general order (mostly for damage skills).
EDIT 2: Fixed a big typo - chakra cost is high -> low, not low -> high
This post was last edited by cra***@gmail.com at 2017-5-10 11:00