I would like to propose the idea of making flyable shuttles equip into unique ship slots.
I think, they should not simply take up a normal ship slot as they do now. if they instead would be slotted, into a ships shuttle bay slot, then we could simply have only as many as our ship can physically fit into its shuttle bay. (I understand I'm talking about a virtual starship thingy here, but it would be more believable if it was realistically limited.)
if it worked this way now, whenever we do finally get the functioning shuttle bays. it will be a way for us to feel like we are getting adequately rewarded for grinding to a new level by also earning more flyable shuttle types to use as well.