In general I find Combat Endurance and Target Analysis to be pretty much mandatory on all my officered ships. CE means +5% damage, +5% top speed and maneuverability, and -5% damage taken, which are all useful buffs. TA is useful because it actually boosts all your damage modifiers, i.e. it's multiplicative with other damage modifiers instead of additive. So, a 100-damage shot with 15% from Ballistic Mastery (elite), 10% bonus from CR, 5% bonus from Tactical Drills, and 20% from TA against a capital, actually means 100 * (1 + 0.15 + 0.1 + 0.05)
*1.2 = 156 damage -- TA actually provides +26 damage on that shot, compared with +30 from the other buffs combined.
Beyond that it really depends. I tend to use long range ships so that means Gunnery Implants and (elite) Ballistic Mastery. Missile Spec if the ship uses missiles, elite if it uses constant fire missiles (but not needed if it just has things like Harpoons). Helmsmanship is very useful for slower ships and faster ships alike. Ordnance Expertise is also useful.
I've generally felt more and more like range is a very valuable stat for the AI because it requires 0 finesse to get full value out of. When I build short range agressive ships, the AI is just not that good at taking advantage of them and spends a ton of time loitering and doing nothing because it can't find openings. Fast/agressive builds are good for handling smaller ships but they just don't get much done against big ships in the hands of the AI in my experience, and they also tend to die much more frequently against end game threats.
I've generally found that player ships are better at high-DPS high-flux ships, whereas AI is better at higher-range higher-capacity ships. AI isn't good at gauging whether or not to commit to going in, which the player is much better at. So for the AI, longer-range weapons are safer to use.
Also, the AI (on both sides) seems to be very sensitive to each ship's % of total flux. So the AI will start turning off weapons if its flux gets high. But conversely, the AI, especially fearless, tends to charge in and launch missiles more often if the opponent is high on flux. This means that to keep the enemy fleet pacified, your ships should try to stay low on flux. That means both good vents
and good flux capacity. I've gotten more mileage out of my AI ships by having them load up on capacity than by loading up on vents. They build up some flux while killing each enemy ship, but they gradually dissipate it before moving on to the next ship, so their overall % flux stays low. This means the enemy ship won't launch their missiles, and die with their missiles largely unused, making them easier to kill.
I actually tend to overflux my AI ships quite a bit but also make sure they have a lot of capacity to handle it.