My go-to is the Aegis or Sidewinder with 2x Missile Turrets, 2x Hardened Systems, 1x Shield Vampire. Aegis has a couple of Power Core Tuners to run the Turrets.
Missile Turret: Accuracy boosts is cumulative. Good against both Shields and Armor and extremely Energy efficient. With high enough Accuracy, you can hit the Star Viper Spearhead 90% of the time while Cloaked. You do need Crew to use them.
Hardened Systems: High Systems makes enemy Shield Vampire/Disruptor and Capacitor Vampire much less likely (or impossible) to land, while guaranteeing your own. It also contributes to Accuracy.
Shield Vampire: I originally got it to style on Teyaal, but it also one-shots the Cyberdale if you use it in the first round (she surrenders if she's out of Shields and doesn't have any remaining decoys).
Holographic Mirror System: Good on the Sidewinder because the holographs are destroyed in 1 hit, but inherit your Evasion. I'd recommend a couple of Thrust Vectoring Systems to boost Evasion further in that case. You also want at least 75 Systems to get 3 images. Higher Systems also protects them against Shield Vampire/Disruptor. It was added after I'd 'finalized' my loadout, so I don't actually use it.
Currently, Modules, Weapons and Crew Capacity are independent, unlike Flash. I don't know if that's a bug or not.
There have been a few posts indicating a Ship combat overhaul is coming, but I don't know when. Almost certainly after the Phaedra II Train Dungeon.
You can now talk to Ship merchants about 'Licensing', which lets Vahn also sell their inventory. Makes buying and upgrading your Ship a lot more convenient.
