Huh, so apparently I never got around to posting here myself... I fly an Apogee; even in mods I've found nothing that I consider to be strictly superior. Initial armament is two heavy blasters and two burst PD, with max vents, dedicated targeting core, unstable injector, and whatever points you have left into capacitors. Final (vanilla) armament tends to be autopulse laser, 2x heavy blaster, proximity charge launcher (for dealing with fighter swarms), 2x tactical laser (in the turrets, also meant as fighter defense), hardened shields, stabilized shields, augmented engines, ITU, 30 vents, and the rest into capacitors.
With mods turned on, things get shaken up a bit; I'm currently running a heavily offensive version that mounts a plasma cannon, a templar Longinus Heavy Laser on the right turret, and a templar Sentenia Assault Cannon on the left turret, with ITU, hardened shields, stabilized shields, augmented engines, 30 vents, 18 capacitors. You kinda have to watch your flux levels with this thing, and use the hold fire button (and have each weapon on its own group so you can make the longinus stop eating your flux vs shielded targets), but it's devastatingly effective.
