The way I'd envisage ship type target priorities would be a ranking order.
I could set that any light frigates will attack the following ship types in descending order of priority:
- Light carriers.
- Capital ships
- Support ships
- Any other military ships
- Military structures
- Anything else
That way, if I tell my whole fleet to attack the enemy's whole fleet, each ship would tend to attack those targets that it's generally most effective against. In a way, such a prioritisation mechanism could even be inbuilt into ships AI (or even already is) but could be a useful tool for the player to customise ahead of battle on their given situation.
Overall ship behaviours would also be useful. Offensive or defensive stance. How closely to cluster as ships. The oldie but goodie Rise of Nations had some nice ideas there (see e.g. here: https://www.youtube.com/watch?v=uB2W8BcUvDY) though Sins 1's fleet manager was pretty decent in that regard. The difficulty might arise if different overall automation command give conflicting advice. For instance, targeting priorites say attack light carriers. But they are far away and behaviour is set to defensive. Should it chase or switch to the next target on the priority list? Similar question if target priority or chase parameter conflict with fleet cohesion overall commands? Leave AoE of beneficial buffs or not? Resolveable problems but they would need some consideration.