I am currently starting to favor ships with very high hull strength. combining an already good base hull/armor on ships like the enforcer, dominator, and lasher with reinforced bulkheads [[ is that something from starsector+? ]] and blast doors allows either you or the AI an immense room for error. Equipping that may reduce overall venting/capacity, but inevitably when the shields on the enforcer/dominator fail due to simply being sub par compared to other ships, I find they take a much larger beating. All officers in fleet have a requirement of at least Damage control 10. Missile spec, Helmsmanship, Gunnery implants, and Power grid modulation come second. Mega bonus points if the ships are XIV variants. After *weeks* of playing, i find myself going back to the basics of the Hegemony fleet doctrine. Simple and reliable ships. The ability to equip dual/single flak cannons and still be able to take any torpedo strike makes them hard to take down.
Funny enough, while i leave those ships in AI control, i usually pilot something completely different. Something mobile that can relocate quickly to help sides of the battlefield that need urgent assistance. If possible, i break out a specific conquest fitting. Mjolnir cannons and Maulers, with burst PD lasers. I don't equip any of the missile launchers, to provide more OP for additional vents and capacitors. I would give it an Integrated targeting unit, unstable injector, and auxiliary thrusters. Depending on what kind of fleet i think i might come up against, I would equip Extended shields and accelerated shields if i expected many wings of bombers/fighters. It is a monster, it out ranges and out DPS's everything the AI can possibly deploy.
1-2 enforcers escorting a free moving dominator with railgun lasher support, and i have a formidable fleet ready for just about anything. I keep all ships equipped with long range weaponry in the main slots, IE Gauss cannons in the slots of the Dominators and Hypervelocity drivers in the enforcers opposite with flak cannons. anything else is equipped with PD. The idea is that the fleet forms a no-mans land wall in-between the two fleets. anything that gets close, gets its shields pounded with kinetic weapons. Thankfully GCs and HVDs are reasonable against armor too, so when the shield drops they get annihilated anyway.
All missiles: Harpoons.
Wait, this thread was about ships and weapon loadouts? uhh, well take my entire fleet. and while your at it, nerf reinforced bulkheads.