I like this idea and would like to participate wherever I can (Story-Lining, simple MOCs, Brain-Stormin, as my brain is sometimes more like a hurricane dating a typhoon rather than a straight directed wind ;-) )
I agree that a consistent story should be included.
And I have an idea on the sub-theme as well:
Asia!
"Normal" Pirates, of course, and Asian ones (for an imagination use the bandits from the old ninja-theme and put them on junks ^.^). It would be a great opportunity to expand the whole pirate setting into the east, make "exotic" looking scenery and buildings and we might as well add some mythical flavor. A Chinese dragon would be an idea, or a big deep sea squid. Would be wonderful in a set together with a smaller vessel trying to escape the vicious tentacles... :)
And as a side note, piracy has been very common in the Asian seas.
Argh! Another idea comes into my mind! Piracy in the Middle Sea! With Arabian/North African pirates in swift ships pretty similar to the pirate ship from "The Lord of the Rings" theme. Lego could re-use some of the molds made for "Price of Persia" and we might see an Arabian harbor as well.
So far, just my 2cents ^.^