There used to be a flux overcharge for higher energy-dps at higher flux levels. Maybe bring it back as a hullmod.
There was, but all the energy weapons were weaker too. Pulse lasers were garbage, and beams had higher OP cost and less range. However, mining blaster was very good back then, good enough to compete with heavy blaster even if a bit worse overall. The damage increase make both pulse lasers and heavy blaster useful (but still not enough to compete with ballistics, except heavy blaster when combined with vent spam, which we will not be able to do anymore). Mining blaster did not get enough of a damage increase, while still keeping exorbitant flux cost. Right now, it is only good as fringe shield overload build for Sunder or AM blaster replacement for Hyperion. Beams got cheaper and more range (except Phase Lance, which lost range).
The only thing I might miss from flux supercharge is the weapons glowing as flux accumulated. It could be interesting if all energy weapons got EMP or minor shield piercing from flux supercharge. Not sure it will be enough to make it worth HUD clutter. Less HUD clutter was the best benefit of flux supercharge removal. Better baseline stats for most energy weapons are good too.
While on the subject of energy weapons, one big advantage they had over ballistics long time ago was unlimited ammo, while ballistics had limited ammo. Sure ballistics were still better than energy, but only when they had ammo. Once ballistics ran out, the ship cannot fight or PD anymore. When ballistics got magazines, energy was still often better or at least competitive because they had a DPS advantage over ballistics. Most ballistics then had small magazines akin to autopulse or TPCs, and were effectively half DPS in prolonged battles. (For me, all important late-game battles are prolonged.) Since ballistics gained unlimited ammo, they are just flat-out better than most energy weapons.