This is something I very much want to do. Instead of creating a separate system to customize the appearance and fighting abilities of your crew, I want to roll this into a concept we call side parties.
The basic idea is that you're the captain of a ship, and while you might occasionally get into a brawl without your trusty crew by your side, most of the time, when you get in a fight, your crew has your back. We haven't worked out the details of how this will work, but the big picture looks something like this:
You have one or more side parties. These side parties are composed of crew from your ship, possibly including ships officers (which is a whole other system), roughly equaling six grunts in effectiveness. Most avatar missions define a number of side parties that you are allowed to take into the mission, and when you enter the mission those parties are waiting for you. Additionally you set one of your side parties to be your boarding crew (with special considerations for large size boarding crew).
When you set up your side parties you can customize a wide variety of things, including appearance, name (within limits), and fighting style. Additionally you can equip bonuses to the crew in your side party, things like special weapons that do more damage, or special training that gives them a new skill. The details of how that would work have not been determined, but the basic idea is that you would be able to specialize and improve your crew with items you acquired through gameplay (likely economic, PvP, and PvE gameplay).
Finally, we want to greatly improve the experience of actually commanding your crew in battle (both boarding and in missions). Currently we're thinking a display that shows the health, balance, and initiative of each member of your side party, as well as a directional arrow, and distance indicator. Commands that can be issued on a per crewman or per side party basis, including movement (stay here, go there, follow me/him), combat (attack him, protect me, protect him, stop fighting), and disposition (fight aggressively, fight defensively, retreat).
I know this steps a bit outside of your original suggestion, but that's what we're currently thinking. What do you think?