Well, you get nifty uniforms from the navy missions if you play long enough. Which is apparently a fairly big draw for many new players (u giv me shoes plz?)

All in all, I think they make decent teaching tools - a lot of new folks need structured "assignments" or they don't know they aren't supposed to just swordfight or hang out in the crowsnest the first few times they board a ship. If the whole game was built around that, I'd agree it was super-RPG-like, but you pretty much run them out quickly and then you're back to looking for your own fun, the way it's always worked, just with more practice at the most common idioms.