I'm surprised to see so many people liking capacitors. The only time I ever put points in capacitors is if I have vents maxed out and I have all the hull mods and weapons I want already, so it's usually only a handful of points if any. Like Commissar said, capacitors only give you a tiny extra buffer before you overload/vent/stop firing. Vents help for everything but permanent flux damage and as such they are always useful unless your shield flux/s + your weapon flux/s total is lower than your dissipation (it happens but rarely). As far as I know they also make active venting faster since active venting is a percentage bonus. Capacitors make active venting take longer as far as I know.
Another thing I feel the need to point out is that the Conquest has medium ballistic slots. To me that screams PUT A DAMN FLAK CANNON IN THERE! If you did that, you probably wouldn't struggle so much with the small shield coverage or the near-uselessness of energy PDs. Once you've made that decision you can then use IR pulse lasers in your small energy slots and deal permanent flux damage at a decent range, or just keep PD in there to make yourself more impervious to missiles. Flak cannons also save you 30 points on the Int. PD AI hull mod if you previously needed it.
Lastly, missiles. I guess I can see why some people like them, but I feel like they're very unreliable in general. Against most lowtech ships and some midtech ones, they get shredded by Flak cannons and machine guns, while against hightech ships most missiles are rendered pointless due to their low damage to shields (exception being the sabots). If you're hitting a hightech ship's armor or hull with missiles, he was dead anyway. It's only my personnal preference but the only missiles I use are swarmers when I have spare OP or lackluster anti-fighter defenses, and Pilums on my long range support ships such as carriers.
EDIT : My current Conquest setup is very "unrefined" as I haven't played with it that much. I use it alongside 1 Condor, 1 Hammerhead and a bunch of Broadswords/Thunders. The setup is the following :
38 flux vents.
Accelerated Shields, Expanded Magazines, Integrated Targetting Unit, Advanced Turret Gyros.
LR PD lasers in all energy slots (including mediums), 4 Flak cannons, 2 Swarmer missile launchers and 4 Storm Needlers. Large missile slots left empty.
Works fine so far but requires more testing and refining on my part.