Scuttle and rebuild - faster.  And no, it shouldn't be faster to build a new ship that to repair a damaged one.

Actually there is one way to heal a ship right away... upgrade a ship to itself. Costs money, though, and it doesn't work if the ship in question is a carrier, because you can't upgrade anything into a Carrier, even if the ship is already a carrier.

There often does come a point where it is cheaper to replace something than it is to fix it and sometimes its faster. But lets also be realistic, when your ship has 1 hp, that does not really mean its limping along with massive holes in 99% of the ship. It means that it is one hit away from hull failure. If you look at a submarine they may be able to take a hit or three and seal up the damaged portions of the vessel but there rapidly comes a point where they can not contain the water. Given the vacuum of space the damage from even a small hole is catastrophic, both in loss of lives in the area from suffocation and in additional internal damage. It should always be faster to repair these ships if they can limp back to a base than it would be to build a massive star ship from scratch. Perhaps a mod can be added to military star bases that adds a module which increases repair rate of docked ships. I don't know how to make such a mod but I would use one and it would give a reason for frontier military star bases. 

I don't think that stardock spent real attention to effective use of your ships. Right now you cannot even see the hitpoints of individual ships in a fleet.

So what I am doing after a fight is separating every single ship from the fleet to see if it is hit in order to regenerate it savely, which again takes ages.
But it's just a waste to send a ship with 10/100 hp into it's death.

But I also agree that there should be more effective ways to heal your ships. However not being able to heal fast might play a part in balancing the defenses. So if ships heal faster, defenses might become worth less and might need to get additional love as well. 

Ship repair and ship upgrading are two things I'd change in GC3. While I would keep the slow healing on the star map to abstract the idea of "repairs while underway" I'd add repair to something shipyards do. Basically have a "repair" option when a ship is 1 hex away that moves it back into the construction queue with the cost being derived from something as simple as (manufacturing cost / total hp) to determine the manufacturing cost of each HP then use that to derive a cost. For example: I have a early fighter that costs 77 MU and has 26.3 HP. Each HP costs 3 MU rounding up. So if I needed to repair say 20 HP it would cost 60 MU and which then would be converted into a construction time in the same way it would if it were being built. If the shipyard only has 5.2 MU per turn for instance, it would take 11 or 12 turns to repair. 

And I'd pretty much handle upgrades the same way, but make them impossible on the star map itself unless there is a construction ship nearby. Just make the manufacturing cost the total cost of the new parts you're adding. It would make it faster than building an entirely new ship in many cases, unless you're replacing every single part. 

This brought to mind a real life example involving a big ship, namely, the repair of the Lexington carrier after the Coral Sea battle in WW2.   The ship took considerable damage and it was estimated that a minimum of two weeks would be required to make it battle worthy.   However, the crews at Pearl worked around the clock and pulled off a minor miracle in roughly 48 hours (not sure I remember the exact time) and made the ship ready for the turning point battle of the Pacific war at Midway.   

Which suggests some things along the lines posted here.    Repairs at shipyards ought not only to be a lot faster, but there should be an option to make a rush repair.   And even in the latter case, the cost of so doing should be much less than rebuilding from scratch.   I suppose one could imagine that "scrapping and rebuilding" really translates as "complete overhaul", but that's not very convincing to me, particularly since if one has a ship somewhat distant one can scrap it there and rebuild and skip the time returning to the shipyard.   

The first repair situation I always face in a game is my original survey ship after a pirate battle.   It seems like just sailing along, even at 1 hp per turn, is more efficient that going back to my home world for repairs and relaunching.   That's largely intuitive, but the idea is that it doesn't "feel right".    Repairing at a shipyard ought to be much faster although it should impact the performance of the shipyard, certainly.   That is, the repair process should just be another entry in the build queue, so nothing is building while repairs are under way.

I love the idea of having accelerated repairs occurring at shipyards and starbases.  I agree that military starbases should have a higher, "bonus" repair factor, or maybe even have the ability to have a full-blown shipyard as an expensive module, only eligible for military starbases.

One other thing, and I think this would add some realism.  This came to mind after reading the post about continuing to use the survey ship even after battle damage from a skirmish with pirates.  Certain types of damage should not "only" result in a reduction of hitpoints.  There should be a chance for reduction in battle or operational effectiveness too, because this is what a tank crew would have to deal with.  This is what a destroyer crew would have to deal with.  This is what a carrier group would have to deal with.  So why not reduce the effectiveness of weapons and defenses, ship range, sensor range, or achievable top speed at various stages of "lost hitpoints", whether randomly or by some other mechanism?

You might win a bad fight, but just like with Army and Navy assets of today, there should be an incentive to engage in repairs.  If your hyperdrive has been damaged (or outright disabled), that would be a good (and realistic) incentive and maybe you need to spend time at a planet or mining starbase to get materials so you can restore partial main power, or some minimal level of hyperdrive so that it doesn't take ten years to get to a real repair facility.  If your armor has been eroded or your shield generators have been discharged, those would be other good (and realistic) incentives.  Get your ship into spacedock for repairs and replenish your crew!

So maybe (based on difficulty factor) for a ship with < 50% available hitpoints, we randomly affect one system, maybe a weapon, or one drive type.  For a ship with < 25% available hitpoints, we randomly affect two systems.  For a ship with < 10% availabe hitpoints, we reduce or eliminate effectiveness of three or more systems.

Maybe some systems can be repaired while underway (sensors and life support), and maybe others can be partially repaired (or not; this could become a bear to model in the game), but we still would need to make for a starbase, colony, or shipyard to effect full repairs.