Didn't have a lot of time with it, but just a bit of quick feedback.
First of all, great stuff overall. Kept getting killed in both of the first two missions, but was progressing so I'm quite sure they're doable. The ships feel very distinct - the Arc Jet burners and the mobility on the destroyer give a neat feel, sort of like a Tempest of the destroyer world.
The cruiser (? flagship in first mission) is great, too - love the Antimatter Lance, and pairing it with the Lucifer system is a fun thing to try to get to work right. I didn't quite manage, but it seems like if you do, the results would be quite worth it.
The projectiles for the Squall Cannon look scaled-up and a bit pixelated - I'd change up the graphics to something else, maybe even a full-on energy bolt like the Onslaught's built-in TPC, or just a new, higher-resolution bullet graphic altogether. The gun has a great feel to it, though, but also seems too strong for a small slot. IMO, would be more appropriate power-wise for a medium, or small with a much longer cooldown.
(I'm guessing you probably based it on the AM Blaster in terms of keeping it balanced - but it's got superior stats in some very important areas (range, higher rate of fire, *much* less flux headroom needed to fire), and more importantly, it's paired with shield-busting kinetics, where the AM Blaster is usually not, due to flux concerns. Consider that a Harpoon does 750 damage per shot - not *that* much more - and it's much easier to counter, where these things are so fast they're almost guaranteed hits when shields so much as flicker down. I get that it's part of the whole package of fragile + superior firepower, so maybe just raising the OP cost somewhat would do. Obviously, just my opinion here, don't feel obligated to change it if you feel otherwise.)
The sound for the Arc Jet has the built-in deactivation, so if you start a burn and then pause the game/switch to the command UI/etc, it'll finish playing out and sound like it shuts off. You probably want to separate the sounds into activation/loop/deactivation - take a look at burndrive.system for how it does it.
The new sounds are really nice, btw. Adds a whole new feeling of freshness to the ships.
Looking forward to seeing where this goes!