Ive noticed some kinda weird things when looking at energy weapons - They often dont actually deal as much damage to shields as they generate flux on your own ship. This extends to some other weapons as well, but mostly energy weapons.
It doesnt seem as bad when you look at weapon stats - The most basic example is a tactical laser. A continuous beam that deals 75 damage at the cost of 75 flux. Energy-type damage means its 1:1 - dealing 75 dps while costing you 75 flux/s
A Burst PD laser is slightly worse off - 46 dps for 56 F/s
As an absolute fringe case, the Antimatter Blaster, dealing a staggering 1,000 burst damage, with a flux cost of 1,500 per shot
Moving up to medium lasers, the absolute best case is the Graviton Beam, dealing 100 (KINETIC) dps with 75F/s. Everything is downhill from here - The Heavy Blaster is 400 dps, for 720 F/s.
Heavy lasers are a bit weird - the Autopulse laser seems to be slightly effective flux wise (204dps ,163F/s), and the High Intensity Laser is 200dps/200 F/s.
Then you have the Plasma Cannon, sitting at 562dps, with 900F/s
As it happens, a lot of higher-tech ships will have a strong damage-flux ratio, often in the .6 range, especially with good crew. If im not mistaken, there is a midrange-OP cost hull modification that modifies this as well. Additionally, flux damage generated from energy weapons does not 'permanently' raise flux in a target - It can always be recovered by passive dissipation with the shields up.
All of this put together means that energy weapons are actually kinda terrible at actually killing stuff - Their main tradeoff being their lack of reliance on ammo(excepting antimatter blaster..), and possibly minor range advantage. In some cases, there is also the instant-hit advantage, but for some (pulse lasers, antimatter blaster, etc) this also isnt the face. Yeah, their point defense abilities with perfect-aim are nice and all..
Even many of the ballistic weapons are kinda odd, dealing 1:1 kinetic damage and flux, with their only benefit being kinetic damage In some cases, not even these will deal more damage to flux on high-tech ships sporting good crews, with proper mods..