One possible problem with relying on "Story Points" to power-up ships is it makes losing them in combat painful. If you really want to keep the ship, that means some form of guaranteed recovery (like Reinforced Bulkheads), and even if you do keep it, it will take (D) mods. If player does not want to pay huge restoration costs, that means much reloading in a difficult fight much like pre-0.8 games.
Hmm - one thought is to make losing ships with perma-mods give you bonus XP. Sort of like how losing ships used to do, but this time not something you'd really want to do on purpose.
I'd like to throw out there that maybe this is a good time to reassess the ship and weapon economy?
My understanding is that ships and weapons sell for near dirt cheap because otherwise it'd be too easy to have players play in an unfun manner where they farm ships and weapons, but-
1. This just leads to players often with an obnoxiously large weapon stockpile and rapid fire clicking through the ship recovery screen 9/10 times.
2. There was a similar rule for trade if I recall, but that system has been reworked to be more intuitive (it makes sense that trading can make you money) and enjoyable (it's not something that's super easy to break and it has some depth).
I really feel that it'd make a lot more sense if weapons beyond the standard affair were much less likely to salvage (due to being more complicated devices) along with enemy ships in general rarely being salvageable (they aren't yours, you don't know the small tweaks their crew made, so it's harder to salvage, irregardless of if it's a common or advanced ship).
Normal players can get most of their Weaponry/Ships through the usual method- Shops for basics, black market/commissions/exploration/colonies for exotics
Players that want to specialize in salvage can dedicate skills, hull mods, ships (salvage gantry anyone?), and maybe even items (marines? "Engineers?") to the process.
With ships being more rare to come by, they can serve as more serious rewards, and the recovery screen is now potentially interesting since even if you don't want a pirate carrier, it can help cover the supply cost of the battle.
It could also mean that dumping your weaponry for cash is a viable solution to short term income problems, or even another way to cover the cost of a battle, rather than just "flat supplies". Hell maybe even a "focus on supplies, or recovery more weaponry" option at the salvage screen. Either way it should help stop the hoarders armory that develops fast and eventually winds up just sitting on the colony (and I still think a "store all weapons" button would be useful either way).