I'd like to see the Bridge Officer and Duty Officer Systems combined a bit. I mean, I have gotten my 1st extra ship (finally reached Lt. Cdr.) Once I reach Admiral and have all these extra ships, why can't I recommend my First officer to their own Command and then assign them missions, just like my duty officers. Also I'd like to be able to promote my Duty Officers to Bridge Officers, especially if each specific DOFF would have a success / failure ratio on assigned missions. Once a certain amount of missions were done with like a 75% success rate you could promote them to Bridge officer status, if you have an open Bridge Officer slot.
The other reason I'd like to see this implemented is to be able to bring my Fleet with me on solo missions, kind of like the way a destroyer group is assigned to a specific Aircraft carrier.
I like the idea, since all of your other ships are sitting around. This will probably make people want to buy more c-store ships.
Also, how about and admiral office? They act like bridges (and visually more customizable) but your captains are there instead, and you can assign high level officers who aren't commanding a ship to give your entire fleet passive bonus.