You've already pointed out other uses where beams are very superior to pulse/ballistic weapons.
...
As you said, there are things that beams are really good at.
Erm, when I was highlighting what beams are best at, it was mainly to point out that they're not entirely useless, not that they're better than other weapons. Compared to other energy weapons, they're at best a decent alternative
in the roles they're best at. You could argue that they're better at taking out fighters and phase ships, but that's a pretty narrow niche. I'd much rather have a Pulse Laser than a Graviton Beam, or an Autopulse Laser than a HIL, because they're better in nearly all circumstances. Even against fighters and phase ships, pulse weapons take care of them easily too.
If you compare energy weapons to ballistics, energy weapons are flatout worse, but that's okay because that's part of the balance. What I'm trying to do with my suggestion is bring beams closer to the level of other energy weapons by making them more generally useful. They'll still be slightly weaker than other energy weapons due to their lower dps which is dealt as soft flux to shields, but that's the tradeoff for accuracy, range, and efficiency.
And beams would be overpowered against high tech frigates.
How would it make beams OP against high-tech frigates? With their flux stats and speed, darting in and out shouldn't be a huge issue, not to mention they themselves could equip beams. With your logic, how are beams not OP against low-tech frigates? If you argue that it's not OP by bringing up armor, I'd like to remind you that frigate armor is weak and finite. It will get burnt away pretty quickly regardless of what weapon is hitting them. The extra flux venting and capacity of a high-tech frigate still gives it a big edge.
Extra rules for certain ships or weapons are always a complication, but if they are applied entirely behind the scenes they can become really confusing. I don't see an obvious way to communicate that beams ignore shield efficiency, you'd probably never figure it out without reading about it (or sitting there with a calculator).
You know what else is an extra rule with extra complications? Soft flux. It's something unique to beam weapons. They already act differently and need a bit of explanation, so I don't see 'requiring a bit of explanation' as a problem.
..high tech ships can't dodge them and its harder to get out of range, so if they ever lower shields they are in for a good deal of pain.
This is true of low-tech ships, too, but it's not like their armor makes them last longer than a high-tech ship's higher flux venting and capacity would. Shield efficiency being equal, I'd even argue that high-tech ships would last longer under beam pressure.
The ballistic weapons have clear roles which you use them in, so why not the same with beams?
Ballistic weapons actually have roles. You normally fit both kinetic and explosive on a single ship and switch between them when the situation calls for it. With energy weapons, beams are just weaker than pulse weapons. There isn't a single circumstance in the base game I can think of where bringing non-PD beam weapons gives a better result than pulse weapons (or pulse weapons and needlers, when possible). Pulse weapons kill. Beam weapons tickle things to death, eventually, if you have enough of them.
I'd like to emphasize that it's specifically against high-tech ships that beam weapons need a boost in order to become worth equipping. Against low-tech ships, they're fine. They're not meant to kill quickly, and by God do they excel at not killing quickly. =p But it takes a disproportionate amount of beam weapons in your fleet to be useful against high-tech ships compared to low-tech ships.
I think I'm not illustrating the points I'm trying to make well enough. So, let's assume that all shields are equally efficient. Beam weapons would still be more effective against low-tech ships than high-tech ships. When a beam hits shields, it generates soft flux. The soft flux it generates would be a smaller proportion of a high-tech ship's flux dissipation compared to a low-tech ship's flux dissipation. High-tech ships also have more flux capacity, so they can be hit by beams longer than low-tech ships without taking hull or armor damage.
Some scenarios:
[Shield efficiency is respected] Against a Balanced Enforcer, two Graviton Beams will generate 480 flux/s. That generates 120% of its flux dissipation and causes it to build up 160f/s (including shield upkeep cost). After 37.5 seconds, the Enforcer will overload or have to drop shields. Against a Point Defense Medusa, two Graviton Beams will generate 240f/s. That generates 48% of its flux dissipation, slowing its dissipation to 140f/s. It won't overload and can continue firing a bit without risking hull damage or an overload.
[Shield efficiency is ignored] Against a Balanced Enforcer, two Graviton Beams will generate 400f/s. This generates 100% of its flux dissipation and causes it to build up 80f/s. After 75 seconds, the Enforcer will overload or have to drop shields. Against a Close Support Medusa, two Graviton Beams will generate 400f/s. That generates 80% of its flux dissipation, causing it to build up 20f/s. After 380 seconds, the Medusa will overload or have to drop shields.
As you can see, ignoring shield efficiency cuts into the high-tech ship a bit harder, but its flux stats still offset the damage enough that its survivability is comparable to the low-tech ship (especially when you take into account the Medusa's ability to pick its fights). The high-tech ship can even keep firing with its shields up if it can find the opportunity to back off and vent occasionally.
If you're still not happy with that, another suggestion would be to use (shield efficiency + 1)/2 to calculate the damage multiplier. Basically, it would only half-ignore shield efficiency. For example, against a shield with .4 efficiency, it would treat it as though it were .7, and .6 would be treated as though it were .8 efficiency. If you're not happy with abstract calculations in this game, I'd like you to remember how armor works. You could have a throwaway line somewhere, maybe in the tutorial, that explains that shield efficiency is partially ignored by beams.
The Graviton Beam is actually ridiculously efficient against shields and would probably need a nerf with this change. In fact, all the non-PD beams might need a slight efficiency nerf with the change. I'm okay with that if it makes them useful, though.