All well and good, the problem came when I captured a Lambda Class Shuttle. I noticed I was always out of supplies. So I ran a little test. Fleet without the shuttle, supple use normal, add in a shuttle, and I am using like 20 supplies a second (with just a couple frigates and a couple of fighter wings.) Not sure what needs to be done to fix it, but there you have it.
I have been unable to replicate this bug. Was this fixed in a Starfarer patch? Are you sure you weren't damaged or over any supply limits?
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Here's a quick progress update:
Empire caps now release TIE squadrons as their ship system. They will be able to unleash a ton of them, though I'm still deciding between giving them regenerating drones or just a very large reserve. As an aside, considering a Star Destroyer in this mod holds 1000-2500 crew, I don't think making fleets lose one crew per fighter destroyed is worth implementing. For now, TIE fighters are also found as normal squadrons in fleets, but don't count on that being the case forever. They are canonically short-ranged fighters, so it makes sense for them to only be found in a SD's retinue.
On the Rebel side, most ships now have High Energy Focus. I intended this to be a temporary placeholder, but I found this system to work well enough that I might keep it. It fits with the 'lining up an attack run' scenes from the films.
While running through the ships, I ran across a few weapons in slots that don't support them. I've only fixed a few of these; I'll carefully inspect the entire mod later. I'm also planning on fixing (read: lowering) the ordnance points available to a few ships, as right now some variants have loads of unused OP.
I feel that Star Wars-style capital ships should be huge, lumbering beasts that mostly fight other capital ships while relying on fighters and frigates to screen them from smaller threats. To that end, I'm considering turning their point defenses into built-in weapons. Quadlasers are fairly terrible (I just watched a veteran Star Destroyer fail to shoot down a single Salamander during the ten seconds it was circling the ship), so I don't think anyone would be too broken up about them not appearing on the loot list. Mostly, this change is because allowing players to replace them with a decent PD system would make this mod's capital ships nigh-unbeatable.