Sounds like you're thinking of an older version, as hired captains don't have carrier specific skills anymore.
Attack focused liuetenants can focus on three areas : missiles, damage, and range as represented by Ballistic Implants, Gunnery Expertise, Target Analysis, Energy Weapon Mastery, and Missile Expertise.
Additionally, there are skills that greatly enhance survivability, like Impact Mitigation, Damage Control, Polarized Armor, and Helmsmanship.
The only really specific skill for any one ship is Field Modulation. You need that bumped up to elite for phase ships. There's not much reason not to.