I can +1 to people having the recovered with story points bug, and for now simply suggest that if you see a ship that has an upgrade you want but it requires SP to get, it might as well be considered that it doesnt have that upgrade, because it won't anymore when you go to recover said upgrade.
For OP, very much like the mod, naturally have a plethora of ideas on how to do things differently but don't want to obscure your vision. As far as constructive points go:
-I agree with the idea that having more exotica mods that change support concepts (ie sensors, sensor profile) would be good, some examples of ideas might be
*[Oversized Sensor Array: More sensor strength, more sensor profile and/or less cargo/crew/fuel space] More/larger arrays collect better signals, but send out more noise and take up space
*[Externally Radiated Systems: Less sensor profile, less hp/armor/shield strength and/or worse flux management capabilities and/or less sensor strength] Having hot ship systems radiating heat/flux externally constantly and locally allows them to maintain some degree of a smaller sensor profile, but opens up vital systems to damage/interferes with typical inbuilt flux systems/causes interference with sensor arrays from increased local noise.
*[Bootstrapped Logistics Compartments: More storage/fuel capacity/crew space, less hp/armor and/or manueverability/speed and or CR cap/recovery rate] Essentially filling non-essential spaces with more storage and strapping additional containers wherever they would fit outside the ship gives more space, but interferes with crew movement, reduces overall structural integrity, and/or increases mass (this one may be largely redundent iyo just because its an additional overhaul to the existing vanilla logistics storage mods of similar, albeit completely positive, function, so largely just spitballing some stuff here).
-I also agree with Ovid that there should be a chance (it wouldnt even have to be too high, something akin to getting AI cores from [REDACTED] ships piloted by them maybe) to get exotics from salvaging ships with exotics without recovering them.
-I actually quite liked the idea of the Alpha core, something that would normally be used either for a pilot or a colonial enhancement, also being able to be used instead for an exotic improvement; with this in mind, what if some other vanilla colonial domain tech could do that, ie Cryoarithmatic engines being used for something that increases accuracy, damage, or fire rate as the ship's flux level rose, almost like the Energy Weapon Mastery Perk? If it was fire rate, it could also prove to be the double edged sword where as you redlined flux to get the dakka you ran a greater risk of overloading your ship (would naturally have to not be overridden by the behaviour that guns wont shoot if they would overload the ship - this could also mean the exotic could be used to allow ships to shoot a weapon they didnt have the flux capacity for normally, but would always overload their ship doing so).
-Not so much an idea, but I've noticed that even for the super high tier, lots of 3 built in upgrade capitol ships Kill Fleets, the number of ships that have exoticas and the level of exoticas they have are often still just three to five ships (often logistics as well) with only one or two upgrades, the impact of which I usually dont notice. That said, the scary stuff is still way more scary, but it all has LOTS of Exoticas, including often multiple exotic techs, so there might be some merit in slightly increasing the likelihood and level of mods on high tier faction fleets (larger raids/expeditions, with Nex the ones that get S-mods since iirc that is a Nex thing, etc) to find a little more of a difficulty middle ground with that. Unfortunately I dont know how hard that would be to implement since I'm a pleb with modding/code, so if it isnt a doable feel free to ignore me in my own ignorance and I apologize.
Mostly ideas, otherwise good work, much wow, super appreciate <3