Apogee does not have much OP to spare. It does not need small weapons at the front. Plasma cannon is probably the best in the large energy, but if you insist on autopulse, get expanded magazines. Apogee does not need PD because of its system - unlimited active flares. Between tough 360 shields and active flares, it does not need PD beams for anti-missile. What it needs is firepower to kill flankers, and IR Pulse Lasers on the small energy mounts would probably be more useful. For the small missile, if I do not put Salamander in it, I leave it empty for more OP. I would not use Augmented Drive Field on Apogee if I have capitals in the fleet.
Astral does not need Locusts, or other weapons for that matter. Bombers and maybe some PD beams should suffice. At least two Longbows and your choice for the other four. None of the fighters in the current release are overpowered enough to compete with bombers.
Atlas and Prometheus has the advantage of taking only one fleet slot. Fleet slots are a premium resource late in the game. If you do not have Navigation, player will need at least two Prometheus to haul capitals a significant distance.
If you do not have Navigation, I recommend keeping Augmented Drive Field on capitals because bringing four or six tugs for speed 20 hurts! Tugs chug fuel and clog valuable fleet slots. Navigation 3 is +2 burn speed, and you can either drop two tugs or Augmented Engines. (I prefer dropping the excess tugs.) Even with Navigation 3 and Augmented Drive Field on capitals, fleet still needs two tugs for speed 20, which is tolerable. When dealing with zombie pirates or other fires in the sector, burn 20 is a must.