Though it would mean that all TSN fighters would be affected, I think this wouldn’t be much of a problem. At the moment, we don’t use fighters at all (or so rarely it is negligable). Individually they are too ineffective and to deploy a group means reducing crews on ships. From my persective the preference seems to be having more bridge crews working together than fewer with lots of fighters.
What would be interesting would be for GMs to manage a supply system that the shuttles could use. This could be simply pop-up messages like ‘medical supplies delivered’ or more complex procedures like transferring ordnance from ships or supply bases (i.e. no space station).
Using shuttles would be mission dependent, but if we drew up situations where they would be needed to be deployed, then we could build them in to missions automatically. E.g. whenever you are transferring personnel to a station, they have to go via shuttle craft.