I'd like to assign them to command vessels when I use photonic fleet and name the vessels as well. It would allow you to tailor photonic fleet a bit more to my play style.
Judging by the AI in this game solo fleets run by NPCs won't work. It will be you alone as your BOFFs captain their ships to get up close for a good look at the Warp Core Breaches.
Q: (Lord-Ice) Is it possible that well ever be able to assign our Bridge Officers to command our alternate ships as AI Space allies?
Dstahl: We have toyed around with the idea that you could assign your First Officer as Captain of one of your other ships and thus have something that is similar to an away team in space, where your Bridge Officer follows you to assist. We believe that this concept fits best with the eventual release of the Admiral rank and are saving it for consideration at that time
This would be something that could also work in tandem with the Doff missions. Rather than your Doffs simply disappearing into the nether when you begin assignments you actually see them embark in shuttles if begun from your ship or even larger vessels if begun from your fleet starbase.
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Dstahl: We have toyed around with the idea that you could assign your First Officer as Captain of one of your other ships and thus have something that is similar to an away team in space, where your Bridge Officer follows you to assist. We believe that this concept fits best with the eventual release of the Admiral rank and are saving it for consideration at that time
http://www.startrekonline.com/node/3223