At the moment, here's how the system works, it's fairly simple I think:
- The baseline cost is I think 1.7/s metal and crystal to repair ships.
- For starship lines, that goes up in cost by 5x, 10x, 15x, or 30x.
- For Golems, it is 40x.
In all cases it is cheaper to repair than to to build anew, so for players that's really all that is needed to be known for decision-making purposes: always repair. In the past, repairs were free, and this costing system was added for 2.0 because some players were abusing the free repairs for starships in particular.
My goal, when modeling all this, was to have a baseline cost that was low but persistent, and that was in general the same for all of the smallish ships. Then for certain abusable ship repairs, mostly starships, to have higher costs based on the increasing costs of those starship lines. Then later in the expansion, I've also used this to give higher repair costs (which are also sort of build costs) to Golems, making their mechanic work.
It is not linear with the cost of building ships because then that would make it so that Teleport Battle Stations were immensely more expensive to repair compared to, say, fighters -- that would cause immeasurable complexity when predicting the resource outflows of engineers doing repairs, amongst a few other complexities.
I very much see where you are coming from, and in some ways your approach is simpler and preferable, but it's one of those things where there is complexity any way you choose, and so you have to "pick your poison" a bit, so to speak. In this case, I picked the one that was simplest in terms of player decision-making (easy choice: always repair over build, paired with the most predictable cost outflows possible for repairs engineers). So that's why I did it that way, anyway!