Probably won't slide but worth a shot.
What if you could actually see your captain and you could get items for your captain to equip hat would boost stats and such. Your captain's race would initially reflect the race you chose. But there could be a special artifact that allows you the change the race of your captain without changing the race of your ship so you'd still have the benefits that you want.
You could get the items from completing x amount of missions along with those artifacts. Then there could be special items you could use GP on. Some items you could make in the CT Lab, etc, etc.
Sound good? bad? needs work? possible?

How about no stats. Just an avatar that people spend real money to dress up ;p

Well that kind've makes it not worth it then. There has to be some common way to get some items for it. As for stats they can be miniscule. Like:
Miner's Jacket: 2% boost to mining or something like that.