The doff system has been a great addition to the game and has done alot to make the player feel like a captain but for alot of us we're not captains we're admirals so my suggestion is since alot of players have ships that are gathering dust in their ship selection you could assign a doff crew to a ship and send it on a long term mission, 3 days for example, for extra cxp or something along those lines.
You could have captain doffs so you could control how many mssion you could run at a time but still have a wide range of mission types plus you feel that at least your doing someting with that T3 thunderchild you bought on the c store
You have an item "Shuttlecraft". It could cost a bundle to make and come in different varieties: Tactical, Engineering and Science.
You could send approximately 5 doffs on a long term mission (i.e. 3 days + ) with this specialized item as a requirement for the mission. As shuttles are expensive, you wouldn't have tons of them.
Once a person reaches the rank of Admiral, then you could then undertake missions at Earth spacedock to commission (unlock) "ships" of various types for your disposal and mission trees to go along with them.