Ahh, Cycerin, you do not disappoint. Awesome work all around.
Criticism, compliments, and riffing on other people's comments, in no particular order:
I agree with LazyWizard about the Fury: it's too much of a simple upgrade to the Reaper. I'll double down on that and say that I don't like the Squilla either—again, too much of an undifferentiated upgrade. Way faster, tougher hull and armor, no omni shield but a much higher flux capacity; it basically just makes the Dagger obsolete. If you tinker with the Fury, that might help to set the Squilla apart, but I don't think just reducing the torpedo's damage will be enough.
I think the fighters are in a good place (it's always a little hard to tell, since you never control them directly). The Krait seems to get the job done in a pretty balanced way, strong against fighters and frigates, tough enough to hang against bigger ships in a support role, but never too overpowering. It is awfully heavily armed on paper, but I think flux keeps that in check. The Serket is a vicious little bastard; the combination of high speed with a phase cloak seems to make them damn near invincible—I don't think I've ever lost a single fighter, no less a whole wing. I actually like that, though; they're very expensive and not outrageously overarmed, and it's a relief not to worry about losing crew. The rockets are a nice touch, giving them a little punch against big ships without tipping the balance in a dogfight or against frigates.
I'll second Meatsteak re: the new Burst Maneuvering Jets; I don't think they're quite where they should be. In open space, you can crank a Desdinova up to like 600 speed (depending on skills, hullmods, etc.), which is fun but not very sensible. The way they work in a nebula is cool, and, from the sounds of it, more like what you had in mind: a sort of low-tech phase skimmer. If it's possible to force the ship back down to its normal cruising speed at the end of a burn, as happens in a nebula, I think you should try that. Otherwise I'd say give the Nevermore a pure maneuvering system to help aim the main gun (maybe tie in energy weapon damage or something) and more traditional jets, as on the Eagle/Falcon, for the others.
I also agree with Meatsteak about the new kinetic weapons—bursty short-range kinetics don't really suit Starsector's shield mechanics; every time you scoot back out of range, the enemy can just drop shields and dissipate that flux. What you want from a kinetic weapon is the ability to keep up constant pressure from a distance, ideally beyond the range of most of your enemy's weapons…so if I learned one thing from trying out different weapon configurations with the BRDY ships, it's that the vanilla Light Needler is completely insane (basically a medium weapon in a small slot), and there's rarely a reason to mount anything else for the shield-breaking role. I propose that you just adopt the all-powerful Light Needler as the official kinetic weapon of BRDY—all hail our new Light Needler overlords, etc. etc. and so forth. Besides, more kinetic weapons is really the last thing the game needs; there are as many vanilla kinetics as there are all other ballistics combined (and that's counting the three varieties of bombs).
If you're looking for ideas for new ballistics to implement, I'd say that frag weapons are quite under-represented (I like Meatsteak's idea of turning the Ironweaver into a micro-flak gun of some kind) and there's probably still room for more medium HE types alongside the (excellent) Squall Cannon.
Elsewhere among the weapons: I like the Argus and the Antiplasma Blaster, although I think it's a bit odd that the latter has better range than any of the existing non-beam medium energy weapons. Maybe take it down to 550 or 600 and boost the damage to compensate? Or would that move it too close to the Mining Blaster?
Quills are awesome, if maybe a teensy bit OP—note that, despite being more accurate and (I think) faster-firing, they actually do more total damage per rack than Annihilators do (but they cost more, too, so maybe fair enough—and they are super fun to use). I'm not sure what to make of the Achilles; it seems awfully expensive for basically just being a weaker, more reliable Sabot. I haven't played with it much, though—it has EMP, right? Does it have a decent chance of causing the new EMP arc effect?
Back to the ships: the Mantis is an absolute monster, my new favorite ship. After fumbling around in a Lasher/Wolf/Vigilance for a while, it's an absolute joy to just fly straight up against a Hound and pound six rockets into its hull, point-blank. It probably needs a nerf, to be honest—maybe a slight reduction in speed, or making the shield frontal—but if it doesn't get one, I certainly won't complain. Great-looking ship, too. Out of curiosity, how did you intend to balance this one? The fluff text implies that the missile-heavy armament is supposed to limit its endurance, but I've had no problems in that regard (and I've been running around with Quills on the universal mounts).
I'll also leap to the defense of the Kurmaraja, which I like a lot, visually and functionally—I've been using one as a flagship. With all due respect to Jonlissla, I actually think the weapon layout is excellent—strong coverage forward and aft, plenty of flexibility with your weapon choices, but also quite restrained, not some completely bananas setup with thirty-seven different turrets. It's actually fairly similar to the Dominator in terms of total firepower, with the Dominator have the edge in medium missile mounts, but the Kurmaraja having the advantage of mounting all its guns as turrets. My one quibble is that the fields of fire for the two missile mounts don't overlap, but in practice it's not really a problem.
Even with the Interdiction Array only in a half-functional state, I've found the Kurmaraja to be a lot of fun. It's by far the fastest ship to mount large ballistic weapons, and whereas the Dominator, Onslaught, and Conquest all have more or less limited fields of fire, the Kurmaraja can aim freely; with Entoptic Rangefinding (or whatever that perk is called), an ITU, and the IA, you can outrange anything in the game, and with those big engines you can move fast enough to maintain that range advantage.
Depending on how the Interdiction Array ends up working, though, the Kurmaraja might end up being a little too well-rounded. I might have misinterpreted the idea behind the IA, but I imagine that, fully functional, it's going to make the Kurmaraja untouchable from long (1000+?) range, forcing enemy ships to come in close. Being (insanely) fast and well-equipped to fight at long range, the Kurmaraja ought to become an awesome anti-capship platform. You'd want its weakness, then, to be smaller ships, right? If strike frigates or fighters get in close, they should be able to chew it apart (I imagine that phase frigates and Hyperions should be the nastiest threats). As it stands, though, the omni-shield, good maneuverability, and all-round weapons coverage mean that even a frigate that sneaks up on my Kurmaraja's stern can't accomplish much. A change to the shield, or maybe just removing two of the rear-facing ballistic mounts, might be enough to solve that potential problem.
Onward! I think the Nevermore is in a really excellent place, balance-wise and fun-wise; it's not easy to use effectively, but really satisfying when everything clicks.
I like the Revenant at 13 FP—it's more fragile than the Venture, and doesn't have the same potential for long-range support, but it's much stronger in close combat. Those Barracudas really can chew a ship apart, given the chance. There's an idea for a new weapon, actually—how about a heavy variant of the Ion Cannon, with 700 range or so? Stick a bunch of needlers on the Revenant's bow, give it an ITU and an Ion Cannon on the medium energy slot, and you can keep the enemy's shields down while using the new Ion Cannon EMP arc thingy to suppress their PD.
Both destroyers are very heavily armored; it works, lore-wise and functionally, for the Gonodactylus, but for the Desdinova I think it's a problem—other people have suggested boosting its FP cost, but I think you should bring down its armor instead, make it more of a glass cannon. As for the shrimp, to be honest, I'm not a fan, but I'll withhold judgement until you've revealed the secrets of the new Hammerclaw.
The Locust is fine, I think. Not every ship needs to be whiz-bang-flashy, and as it stands the Locust would actually make a very good starting ship—it's quite strong not just against fighters but 1-on-1 against other frigates too, especially slower ones. Still, it wouldn't hurt to either knock one FP off the price tag or crank the speed up just a wee bit to emphasize its strength in that department.
The Scarab's good, too. Very nicely balanced, with the crappy shield and poor PD coverage matched against the strong hull and heavy armament.
And I think that's everything!