What if we had an option to use AI Cores in ships just like we can do in colonies?
The AI cores would have every skill that affects piloted ship (same as officers) at the level corresponding to their rarity
Gamma AI core: lv1
Beta AI core: lv2
Alpha AI core: lv3
Off course there would be drawbacks, Hegemony, the Church and other anti-AI factions would be able to detect the cores while scanning your ships, also using the cores automatically would raise suspicion over time as you remain in the sector, if detected the patrol would demand the whole ship to be handed over to be destroyed and would occur loss of reputation
Spoiler
But wait, there is more
Using An Alpha AI would be particularly dangerous in three ways:
-First the AI core sense of self-preservation would trump your orders during combat, causing the ship to fall back, act timid or even automatically retreat if threatened
-The second case of possible betrayal would be when you are ambushed by a much stronger fleet (5 stars+) the AI ship would split away from your fleet before the combat and become a Rogue Remnant Fleet, and it would travel to the nearest Remnant system
-The worst case would be if you had more than half of your fleet controlled by AI and you have at least one Alpha AI equipped, there would be a small chance while travelling through deep hyperspace or when you are alone in a sector that the Alpha AI would take over all other AI cores and throw a mutiny, splitting your fleet into human controlled and AI controlled, the AI would thank you for the wonderful ships and leave to become a Rogue Remnant Fleet, you would have a chance of engaging and destroying the fleet during the dialog, but every ship would have a Faulty Rogue AI Damage mod in it if recovered.