I use frigates with most weapon slots and fill them with missles for long range missle fire, minimal shields and minial engines. These sit in the back well away from the enemy and provide a powerful firebase.
Heavy ships up front, Minimal engines, light armor a strong mix of lazer types for mid range, mix type of strong shields. Advance targeting, Advance shield regen. Any spare slots are filled up with anti fighter or more llikely mid range missles.
Anti fighter frigates, mid shields, light armor, anti fighter defences, easily take down enemy fighters and bombers. These sit just behind the big boys on mission where enemy uses fighters and safely swat down small fighters but are useless once it complete its role for the rest of the battle.
Given how many MMOs you play Mobboss you should have no problem with number/stat crunching you ideal ship and fleet. But I cleared all misson on hardest difficulty with my build handily