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I believe this has been discussed before, and while a valid point, doesn't really make a lot of sense, so please forgive my bluntness.
If I remember correctly, the point I made the last time I saw this suggestion was something along the lines of, "You would never take your car to a repair shop and say 'Fix the flat tire but leave the smashed windscreen how it is - I like it that way.'" Just imagine the reaction you would get.
That's how I see the restoration of ships, anyway. Being able to select specific mods to be fixed, while undoubtedly useful, also defeats some of the purpose of the macro-mechanic and just doesn't make logical sense.
It's a really bad analogy. First off if you got a crashed or damaged car you got a choice - to fix it with brand new parts or used ones. Or better, "hammer" it out in some cases. And everyone knows that "hammered out" or used parts ARE WORSE and the car fixed in that way will not provide the same level of security as a brand new one. It's especially true in any sort of crash as if you wanted really fix (or restore) you'd would truly have to just buy a new one as the crashed car frame's is just weaker from now on no matter what you'll do to the rest of the vehicle -it won't provide the same level of security anymore. There's a reason why people even hire specialists to inspect the used cars to find out have they been crashed in the past. As they might have been "restored" but they'll just fold up and smash whoever is driving them upon an accident.
So I'm sorry but your contr-argument is inherently flawed in my opinion.
As for the suggestion itself. I think it could and SHOULD be done. Going further with your car analogy, I think it could be done also in an interesting manner as different parts would have different costs associated with them. Armor, being external part would be the cheapest to restore while things like internal structure or engines would have to be the ones most costly (perhaps reaching beyond 50% of the brand new ship price tag, so with just 2 d-mods it would be already cheaper to buy a new one but having d-mods like broken armor and damaged weapon mounts [ik that Alex removes it now but it's just an example] although just as crippling wouldn't cost more than a new ship). On top of that I think ship fixed that way could have slightly worse stats in few departments (flux management, armor, hull strength - not speed as fixing that part would mean installing a completely new engine [which would also cost a small fortune in itself btw]) too after the repairs. In short this system could be really fleshed out to be a major part of the game not just a gimmick that comes into play when you find a rare ship you absolutely want.
Anyway, if done in a such way it would be more immersive and would give more incentives to use ships that ain't new. Especially if the costs of the new ones would be risen, which is totally different topic but being honest - ship cost plays a role only early on in the game. Later the only obstacle is finding a desired ship really - not actually buying it. This part should also be addressed upon touching the restoration mechanics and fleshing them out.
All of this is a mute point for now however.
