Just a quick extension of my earlier thoughts regarding overused cliches and using history in videogames.
Two great tastes that should seemingly taste great together - but for some reason are not well-represented. Yes, yes, I know Sid Meier's Pirates! was a brilliant gem of design; Now name another great pirate game (and not the recent remake of Pirates!).
I think one of the deficiencies of pirate games is that they rely, not on solid stories, but on ideas that have become well-known cliches, at least in America. The eyepatch, the parrot on the shoulder, the pegleg, Davy Jones's locker, the Skull and Crossbones - these are agreed-upon symbols. We know that the presence of these images are meant to evoke piracy in our minds.
But pirate games deal only with the surface of being a pirate, the types of things that five-year-olds regularly imagine.
Why not bring sophistication to the genre?
This site presents lots of rich details to mine for gameplay ideas.
Pirate flags may have been used to strike fear into enemies. Let's say the more success you have while you fly your black flag, the more ships will surrender to you without violence; However, the longer it is in use, the more you will attract bounty hunters eager to stop you. You would also have an option before combat to fly a red flag, which states that no quarter will be given - depending on the enemy, this could have a motivating or demoralizing effect.
What about letting a captain set a code of conduct, which would have varying effects on your crew? You could adjust the shares each member receives, regulations on alcohol, women, swearing, religion - and all of those things could cause profound changes to the morale of your vessel.
Let me play a pirate who treats his crew as democratic members of a collective, who attacks slave ships, frees the captives and kills the slavers as a warning, who sends assassins against corrupt government officials, who sets up ancient greek-like city-states among the Carribbean islands. An educated man, a champion of freedom, yet brutal in meting out justice.
So let's try to reign in those cliches like a wayward yardarm, eh, Maties? Else I'm forced to keel-haul ye!