Just an aside:
I solved the problems with Frag in Rebal by making Frag do normal Flux damage vs. Form Shields. This gave Form Shields (universally used by Fighters in Rebal) a signal disadvantage vs. Frag, which in turn gave Frag a distinct point... as well as letting players use Thumpers (which are kind of auto-shotguns in Rebal) to spank enemies using Form Shields with very efficient counters. All of this fixed the major problems with Frag's concept and balance; I think it's worth using there.
To solve this in a more Vanilla-ish way:
Have a special rule for Frag, where they do quad damage vs. fighters (including Armor and Shields) and missiles and double damage against normal Hull, but aren't efficient for Flux-trading or killing Armor. This would be in line with the other weapon types' special rules, and therefore less confusing, while making it totally clear what Frag's designed to do.
I.E., you could take a Thumper, make it 0.75 efficient (before miss-rates and all that) so that it's an unattractive weapon except against the targets it's meant to eat alive. Nobody will use it for anything but the stated purpose; killing Fighters. But it could be very good at that (IDK whether 4X damage would get it there, but probably). The problem with the Thumper is there's absolutely nothing it's good enough at that I'd use one, period; having a straight-up Ballistic solution to fighters sounds like a good solution.
This would, of course, require a completely different set of stats for Frag weapons, especially the AOE stuff, but it's the AOE (reducing miss-rates very considerably) that has to be accounted for, not the damage per se, but it's not a big deal, honestly.
I think this is the right way to solve this problem. Frag's been kept the same since Fighters largely didn't have Armor, let alone Shields; as time has passed, it's become almost entirely about its role as Flux-efficient PD. Give it a bonus vs. Fighters and missiles explicitly and now it's a nice solid niche.
The other possible Vanilla-ish solutions would be:
Remove the Thumper or change it to another type entirely. The Thumper has been on the list, of "top 10 weapons I'd never mount for serious play" since 0.54, lol. Other than nostalgia, nobody will miss it.
Buff Thumper for no particular reason, then nerf again in 9 months when somebody figures out a niche build that works, like shieldless Enforcers with five of them or something equally ridiculous, lol.
Get rid of Armor for Fighters, buffing hitpoints where it's reasonable to keep Low Tech viable. High Tech Fighters still have a major advantage vs. Low Tech PD, but it's not as egregious and they'll get killed if they run out of Flux.
Oh, and whoever said that Locusts aren't the best missile... honestly, I think you may want to mess with them more. They're the best missile atm. Really. Because they do the two things missiles should be really good for: killing smaller threats and wasting enemy Flux killing them off. That second part is why they're pretty awesome, honestly; a Locust swarm in the midst of the enemy can lay waste to more Flux indirectly than any weapon in the game, other than perhaps a perfect Sabot strike, can directly. In a game where Flux-locking is the main objective, that's a win.