Ok hear me out first. This is only an idea i played with and it could've even be considered already. If that's the case I'm sorry. It's something I thought would be a new challenge for the playstyle as it would add quite a lot to the difficulty of the game. Please read first before commenting:
alright this is just a idea to add more versatility to a ship. Eve Online players might be familiar with this as it would work quite in the same manner. Rigs would be permanent ship modification (as in a new slot) that provide bonuses to various ship functions. There could be one or two different rigs installed in a ship. not the same ones twice though. Some examples what they would do:
Hull Rig
+Reduces hits on the hull to repair it. by factor x
-Reduced armor health points by factor x
Armor Rig
+Adds more armor by factor x
-Makes ship heavier and therefor slower and less maneuverable
Alluminium Structure
+makes ship lighter and and therefor faster and more maneuverable
-ship is now briddle and more affected by fire (as the multing-point is very low)
reinforced silk balloon
+the ballon becomes more armored and sturdy. Perhaps even Invulnerable to Fire
-Ship is more likely to cacth fire (as gasoline drops from it) and altitude can't be changed as fast
Upgraded gun reloading engine
+all guns will have faster reloading speed by factor x
-Turning speed and angle is reduced by factor x
Now then, as you can see this would add something to the ship while it makes it more vulnerable at other stuff. Needless to say this is an option for your ship. The new Challenge would be to counter the other ship with a fitting loadout. For example you counter a Armor rigged ship with a aluminum structure. Think yourself of more possibilities and rigs. And yes new Metaships would probably emerge from that. But with the right balancing this could be prohibited.
I know this would change quite a bit on the game so I'm really not expecting this to happen any time soon nor is it thought through very well yet. This would require heavy balancing first. But for me this would make the ship even more unique and different from the others. Imagine if this would be an option for your ship, what would you add or how would it affect your game? Let your creativity flow.