While I don't plan to use the special abilities associated with the Ship Roles found in Into the Storm , it did seem useful to me to use the Roles themselves them as a baseline when developing a shipboard hierarchy. Apart from assisting players in determining their roles, it provides some useful guides as to which NPCs it's worth developing, and also goes a long way towards creating a feel for the structure of the vessel.
The end result can be found here, for anyone who might find it useful: