I thought it was cool on the first featured series where the Doff system was integrated into the mission. It made me wonder if you could expand that functionality to the ship interiors. What if you could walk around your ship and interface with consols to get Doff missions. You go to engineering and you use a console or NPC and access engineering Doff missions. You go to the bridge and get espionage missions, sickbay for medical missions etc. I think it would give us some more interaction on the ship interior.
Further to this, what if you added a logistical constraint on the Doff missions? For some missions you have to pick a shuttle from your inventory. Different shuttles offer different stats. Faster shuttles offer shorter missions, stronger shuttles offer less injury risk. From a star base you can change your shuttle inventory.