The only thing that irks me about this game is loosing a ship, especially early on. Usually my fleet would consist of a small bunch that i can pilot/command effectively to take on targets somewhat larger. It is quite a blow to loose a ship there, where a single ship is a large portion of my combat capability. Most of the time in this game i will go for the points in the tech tree and go for the one that increases the chances of having a disabled ship re-activate itself so there would be a chance i could recover, but it kind of sucks when it is all up to RNG at that point. And the rare hulls being of course very rare, it sucks to have to re find something like an apogee x.x
The only thing i could think up to change would be to emphasize the difference between "disabled" and "destroyed". Ships that were destroyed in battle would be gone, but ships that were only disabled could be repaired and recovered if you still had control over the battlefield after the engagement. So if you lost something as important as your second frigate in the early game, but still won the battle, you could tow the wreck back to a port to have it repaired. Possibly it could retain some sort of permanent damage, if it was repaired at a sub par port. [ cough pirates cough ] Crew and modules lost would work the same way it does now, but it would still cost a pretty penny to repair a ship all the way from 1% hull/armor.
At the moment, disabled is a probably dead and destroyed is a definitely dead and it kind of drives me nuts sometimes