I feel that numerous goals can be tied together with an updated damage and repairs system. We want ships to feel like important, permanent investments that you don't acquire or lose lightly. This can coincide with a decrease of availability and an increase in price to add soul, weight, and importance to ships. At the same time, ships should be costly and make sudden fleet growth more difficult, prolonging the experience of the game via progression. And while we're at it, the cost of defeat can be mitigated from total loss to a setback by letting defeated ships limp back home.
How can this be done?
Take the current system: ships lose CR by entering battle, sometimes during battle, and (if hull is damaged or the fleet is harried) after battle, on average about 30% CR. Hull and armor can also be damaged; some ships come home with no damage, others can have nearly 100% damage. On average it ends up being roughly equal to CR loss in cost (though, repairing from 0 is generally more expensive than recovering from 0). Both types of damage (CR and Repairs) end up on the same bill, the total cost of recovery is merely the worse of the two rather than the sum of the two. As a result, recovering nearly-destroyed ships costs quite a bit, but the general wear and tear of battle is fairly easy to circumvent. Stations giving instant repairs doesn't help, either. And if a ship hits 0, which they often do, it is more often than not gone... Until later in the game where you have skills to make that chance higher -- when you no longer really need it.
First things first: making ships stick around longer. Ultimately, making the ship merely more likely to repair after battle is lame and detached from the reality of the battle: it freaking exploded! Once a ship blows up like that, it should be a lost cause, or at least future scrap or a D variant. Instead, ships would have a transitional state between hitting 0 hull and actually blowing up and becoming a "disabled" hulk. Let's call this "crippled". To represent hit points in this state, which would be some function of max hull rather than an advertised stat, a gray bar is used instead of red or green. While crippled, other AIs treat it as living for the purposes of pathfinding and such, and friendly AI will avoid shooting it, and it is still a valid escort target. Enemy AI would depend on their disposition to you: pirates would avoid shooting it because they want to capture it, but the Luddic church would make sure to blast that cursed technology to slag. When crippled, a ship would act as if it was overloaded with the added penalty of having engines malfunction all the time. In addition, being crippled would cause a flame-out. It can eventually limp away but not that much else.
Crippled ships would be the norm as far as casualties are concerned; the ship would be unable to continue fighting but would have a logical reason for returning alive. It could also tie into reputation; crippling enemy ships would not make you drop as much as if you outright disabled or destroyed them. Maybe you could give a standing order to your fleet to annihilate the enemy, leaving nothing alive -- making it more likely for the enemy to retreat and leave you with salvage to pick up.
The crippled state would be repaired before anything else on the ship, and until it is no longer crippled, the ship would act as if it were mothballed and have a steep burn speed penalty. This would drill in the feeling of limping back home and make the decision to "leave it behind" (scuttling) viable. Plus it would give an excuse to have better pacing for escape scenarios, as you would not be that worried about your fast and healthy fleet members, but you would definitely need to put in work to save your crippled ships.
This can also tie into officer death, at some point; if the officer's ship is crippled, you can ride in like a knight and save his ass from the fire. The player would feel like they have agency and importance by being able to make a solid impact on their own fleet's survival, rather than hoping the fickle hand of the AI RNG will spare their ships this time.
Plus, it cuts down on save scumming because crippled ships would be a temporary rather than a permanent setback.