Remote piloting needs a stable and continuous communication with the vehicle: should we have some mechanics to model the (active) interference against it, to reduce its effectiveness? as well as to model the means for defending against disturbance.
It’s not simply application of ECM and ECCM.
IMO, it would be too much micromanagement for small to zero in-game advantages/fun.
So, if we wish, we can focus on AI-driven ships.
But, I think they would need new in-game mechanics, and standing and conditional orders to program their general behaviour. Because, if they are AI-driven, why should we, simple humans 
, issue step-by-step orders to them?
E.g., for armed ships: move to a system with alien presence and engage them. How to engage and how to defend should be left to the AI of the ship. In-game.
Or haven’t I understood what you are asking / talking about?
Another thought about possible ships automation mechanics is to add a tech line, starting with the very ability of making automated space combat vessels, and then adding combat AI bonuses up to the level (at the final tech) of the maximum bonuses for “natural” commanders.
So, the difference would be quite realistic and meaningful:
- you’d have anyway a wide collection of commanders with different skills and reflexes with a nearly zero cost of building this pool up;
- you’d have an option of investing a lot of research into combat AI to have guaranteed combat bonuses (in addition to the instant reaction) without picking up the best from the natural beings pool, with a perspective of having always the best combat intellect possible at the end of this long way;
- your population may not trust AI enough, so you’d still need manned combatants to prevent population from raging into The Butlerian Jihad, and so maybe it’s better to use the manned fleet you need anyway and not invest in a fleet you’d have so much problems with just because it would be a bit better during combat;
- in some cases, like frontier surveyors or JP blockading/assaulting fleets, you may choose AI ships, even low-tech (and so not very good) ones, just to bother less about living crew long isolation and losses (for those playing a role).
And another thought is to make AI ships more vulnerable to some types of weapons / damage typed, in wich case I think the natural candidates are HPMW and Mesons and, possibly, some spoiler EW able to hack your AI.
We don’t have to issue step-by-step orders to our human commanders too, it’s just that we need to pretend for ourselves we ARE these commanders, switching roles turn by turn.
Honestly, having AI Navy combatants is not a thing I need much as such, and I think this feature, would it be implemented, needs to be switchable at the campaign level, because for the most popular settings (WH40K, Starfire, Star Trek etc) combat AI is quite alien (I never play with these popular settings, my preference for SciFi is much more hardcore, yet these are still the most popular for Aurora players and for Steve in particular, and so any suggestion have to be consistent with these settings primarily). What makes me think it’s still needed in Aurora is a particular spoiler, wich is already in the game, while having the same crew mechanics as all the rest, and it fits visibly cranky.
What bothers me personally much more is that while I cannot avoid checking crew numbers for the ship while designing, these numbers inflict disbelieve, especially when I try to tinker engines. Large engines do not need hundreds of mechanics even now, and the tendency is clear that this need is lowering steadily. Large thermonuclear (and even more advanced) space engines with crews of 150-200 men each when our nuclear submarine engines of nearly the same volume need just several mechanic specialists for their long months of submerged missions is a real issue for me. It’s obvious Steve do not think it’s a problem, so the other way for me to solve this my personal issue is to use AI ships would they be implemented, even if it means throwing live commanders with their personal histories out of window completely.
One thing I’d like unmanned vessels for is jump point probes. Of course I celebrate the sacrifice of the glorious jump scouts, but I think they would appreciate it if it was unnecessary.
Unless a new capability for missiles to enter jump point were added, though that might cause balance issues.
Edit: although maybe not that much if they also suffer from jump shock. I suppose they’d get gunned down pretty quickly before they could descramble any onboard sensor and aquire a target/deploy a mine if a fleet is parked there.
Jump missile pods are Starfire OG