I remember reading fairly recently about an idea that's been floating around about being able to do more with your first officer, including the potential for him to be in command of a ship.
I think that Vice Admirals should be able to have at least one adjutant, and it could be fairly easy to implement.
First, you'd have to have a commander level bridge officer, so you can promote him to captain so he can be your adjutant. This guy should automatically follow you down to New Romulus and any other zone like it (I assume more are forthcoming).
But in addition to being able to bring him along with you on ground missions, you should be able to outfit him in one of your ships! If there was a second button next to the "set current" on the ship selection menu you could activate it for him. How you could use this new NPC ship seems sort of natural. Instead of the normal distress call, you could call your own ship in. I know this might conflict with the upcoming romulan and reman distress calls in Season 7, so maybe the adjutant ship could be limited to certain PvE missions.
One feature that I would like to see in addition to the aforementioned would be some type of control over the NPC. I think the carrier pet commands could be extended to all ship pets (including saucer sections and other multi-vector modules), as well as the NPC ship. It would be nice to have an NPC with some nifty weapons covering my back while I work on destroying a specific target. The runabouts do a great job on intercept, I hope that my adjutant could come through in similar fashion!
Just my $0.02. I'm definitely looking forward to Season 7, and am excited to outfit my boffs with gear and abilities they'll use.