Michael Hammer has suggested some interesting new rules, but I think we have to be careful about making things more complicated - the more rules/attributes/skills there are the more difficult it is for new players or potential players to understand, and the more difficult it is for the Gamemasters is to administer and keep track of things - and we really want happy gamesmasters 'cos without them there is no game!
I think that new rules should only be introduced if they are simple, fun and add potential to the roleplaying. Keep bureaucracy to a minimum.
Having said that, I like Michael's idea of "special missions", like exploration or capturing pirates. Perhaps it could be done by extending the range of "independant actions" that a volunteer ship or blockade sloop can do. Or, like East India sailings, the Gamesmasters could have a ship comissioned specially every so often, and invite volunteers aboard.
Andy