I know this could be changing some core mechanics, but I'll give it a try.
There could be a module that adds crew stations to the ship - number of stations defined by module class - increasing the multicrew limit.
Create a rule that in order for a SLF to work, there should be a crew station and a bay, and allow ships to have multiple fighter hangars and crew station modules, so the player can find the best build. The module could be heavy on energy consumption, to avoid abuse.
That could create an entire new gameplay, with some ships being more suited for this, becoming small carriers.
There could be a module that adds crew stations to the ship - number of stations defined by module class - increasing the multicrew limit.
Create a rule that in order for a SLF to work, there should be a crew station and a bay, and allow ships to have multiple fighter hangars and crew station modules, so the player can find the best build. The module could be heavy on energy consumption, to avoid abuse.
That could create an entire new gameplay, with some ships being more suited for this, becoming small carriers.