Greetings,
I am a relatively new player, but I love the game and I've been told that Devs do actually read these things so here is my suggestion:
I. Engineer player(s) can assign Engineer AIs to specific areas or components of the ship.
Pros -
1. Avoids AIs wasting time running around the ship and stepping on the toes of the player engineer (really bad on the Mobula!)
2. this gives Engineering players a feeling of being Chief Engineer - nice!
Cons -
1. this gives engineering players another task to juggle
2. conflict resolution with orders from multiple players. . . but if you have 2 engineer players and AI is on engineering too you've got bigger problems.
II. This can be overridden by the Captain's commands to AIs (but is persistent when they switch back to Engineering duty) - In other words, Chain of Command.
Thanks!