I like the idea to have a choice in naming your own ship. There are going to be thousands of captains in this game so having 2000+ ships with the name 'Constitution' sailing the high seas would be confusing and a bit annoying. Kind of like an "I'm Spartacus" scenario.
I don't know how naming your ship could be implimented, either through a name-generator or through an obscenity filter. All I know is that I'd like to be able to give my ship an unique name.