...or at the very least to be able to pick which class they play.
Being able to assign them to specific guns/components would be nice as well.
I don't know if being able to change their loadout is that important as the game currently stands though.. at least, not if they're a gunner - unless you have control over which ammo type they use from moment to moment, it's just going to be pretty much random.
As engineers it might make a slight difference in how fast they can repair things, but other than swapping the extinguisher for the chemical spray, the only other thing you can do really is swap out the mallet and spanner for a pipe wrench in order to free up a slot for a buff hammer, which at the moment would be pretty useless since currently the AI splits its time between repairing and sitting on guns (which means in order for this to be of any use, they need to not only add in the ability for you to pick specific locations for the AI to work, but also a way to pick the tool they are currently using - fine for quiet times, but it might be tricky to do under fire.. most people have their hands full with their own roles, let alone managing someone elses.).
Still, if they managed to integrate some kind of simple AI quick menu that you could bring up, being able to customize the AI players would be good.
What might be interesting is if, once an AI is assigned to a role, they are 'partnered' with a player of similar role who then has control over their actions.. so an Engineer would get an assistant who they can point at a component and say 'fix/buff' or send to a gun, and Gunners could do the same but with control over ammo types.
Possibly the ability to chain commands would be useful as well.. so you could look at an engine, target it for the AI to fix/buff, then look over at another engine or component and highlight that as well, meaning you wouldn't have to babysit the AI since it would carry out your list of commands before going back on automatic/reporting back to you.
I know some people might think this should be the Captain/Pilots job since they're in command, but it might be tricky if they can't see the areas they're assigning to - it would require a more complicated UI than simply looking at the area in question and pressing a button, and I know how many people around here are opposed to adding to the UI.
If additional control is being added, it would also make sense to be able to assign specific targets, so the AI isn't the only member of the ship not shooting at the primary target.
I can see this being a Captain command, but it would make sense that the controllers of the 'assistants' would be able to override it if necessary.