After playing this game for a reasonable amount of time and experimenting with almost every ship and weapon, I came to a conclusion that the medium energy slot is a clear loser on a otherwise very balanced arsenal available to the player, with very rare exceptions. To reinforce this idea I will present my general thoughts on all slots and some of the choices I've found to work, then elaborate on medium energy and why I think it needs some love.
Small Ballistics: Great slot. Extremely versatile, with many options for PD, short range or medium range kinetic, frag and high explosive damage. Vulcan Cannons are some of the best PD in the game, railguns are amazing kinetic pressure. Light Mortars aren't amazing IMO but they are an option if you want explosive dmg.
Medium Ballistics: Amazing. Just as versatile as small ballistics, but with more options, on top of short and medium range frag, kinetic and HE damage you also get amazing long range options. Hypervelocity Drivers and Heavy Maulers are some of the best weapons in the game for long range kinetic and HE damage respectively, Heavy Autocannons and Heavy Mortars do the same on medium range, Assault Chainguns are great for close quarters combat, Flak and Dual Flak Cannons are amazing PD, Heavy Machine Guns can be good kinetic pressure on QCQ ships with Safety Overrides.
Large Ballistics: Good. Not as versatile as the other slots, as most your options are long range, but they are still great options nonetheless. Devastator Cannons are probably the best PD weapon in the game, all the High Explosive options are good on their own rights, Gauss cannons are amazing kinetic pressure with insane range, Mjolnir cannons do decent energy damage from afar with a EMP on top.
Small Energy: Good slot. many pd options, all of which are good though I prefer the Burst PD Laser, Antimatter Blasters are amazing on QCQ ships, frigates, destroyers, cruisers, anything fast or phase can use one. Ion cannons are also good on QCQ ships, EMP is never a bad thing to have. Tactical Lasers aren't amazing IMO but if you're building a very long range ship with beam weapons, targeting core/unit and advanced optics you might as well slap some of those in for extra damage.
Large Energy: Amazing slot. Great mid range energy DPS options on the Plasma Cannons and Autopulse Lasers, and the amazing Tachyon Lances to poke and EMP your enemy at a distance.
Missiles need no explanation, pretty much every single missile weapon is good on their own right with very few exceptions, if any. These are the best weapons until they run out of ammo.
Which brings us to the point I'm trying to make: The Medium Energy Slot. I'd like to start off by saying the Graviton Beam and the Ion Beam are great support weapons, if not some of the best. Constant kinetic and EMP pressure is never bad. However the med energy slot lacks outstanding damage dealing options, as the Heavy Blaster is extremely flux hungry and short range, the Ion Pulser is good at very short range but the AI struggles greatly to use it because of the magazine size, Phase Lances do extremely low DPS, Pulse Lasers are just unimpressive in every possible aspect, and the energy damage type tends to struggle greatly vs armour, and the late game ships are all heavily armoured.
Furthermore, some ships seem to have been designed to rely on the medium energy slots for damage, like the Fury and the Medusa, and I often struggle to build these ships around said slots, despite of their great stats. Falcons and Eagles also feel weak since those two medium energy slots are rarely doing much other then providing a slight kinetic pressure or a weak EMP bean. The mediocrity of the Medium Energy slot also makes high tech ships often rely on missiles instead of energy weapons. The Aurora is an amazing hull, with SO and missiles it can easily take down most capitals in the game, but trying one without missiles, relying instead on energy weapons is often lackluster. The Midline and Low Tech cruisers comparable to the Aurora don't suffer from this problem, as Eradicators and Champions can easily forfeit missiles altogether to rely on Hypervelocity Drivers, Heavy Maulers or assault Chainguns for damage.
Also its important to point out that [VERY REDACTED] weapons make this slot good but they are so limited and hard to acquire I prefer to not include them in the general weaponry available.
In conclusion, my suggestion is either a stat buff to the standard damage dealing weapons in the class, which are the Heavy Blaster (preferably a range buff) and the Pulse Lasers (I dont know what to buff on this one), or even add a new weapon to bolster the strength of this slot.