Your flying and Ody and you have the aux craft console in place. You get DOFF assignments about sending your aux craft on a little mission. From a business point of view this is another way to encourage store sales of ships.
If your in a carrier you get an assignment for the specific carrier pet in use. So the assignment actually mentions your pet, as if your pet is THE pet (shuttles or whatever) for the job.
If your in a vessel that has saucer separation you could get a doff assignment that that says something about leaving the saucer behind with most of the ships crew while something highly dangerous is investigated or dealt with.
Not saying they actually get sent like you don't have them during battle but its just the Star Trek feel factor I'm thinking about. Tying our ship and Captain into the doff system a bit more. Right now it is really just our boffs acting as chiefs and that is more like a setting.
It could go a step further. Assignments related to what our ship can do, the consoles it has on it, mainly c-store consoles i.e. Assignment for repairing Point Defense System which gives that console a buff, assignment for collecting parts from New Romulus to repair a Romulan related console from the Rep system.
i would like, however, class specific exploration missions and episodic missions.
Class specific would be sweet.
Assignments that can be done prior to a mission would be cool, such as intelligence gathering and get buffs for that mission alone. That sort of approach could be episodically along side the actual episodes. Totally optional.
Cryptic must have something planned already, be nice to get some hints.