This was just posted on the Pirate101 Forums from Blind Mew, the KI developer, hinting that Chapter 13 of the main story will "be a bit darker [than] what we've done before, and it's definitely a war story." This may mean anything, but it seems to support a trip to Marleybone, given the PC's role in starting a major conflict between Valencia and Marleybone during our romp in Port Royale with Catbeard. No way to know for certain, but it would be a good idea, narrative-wise, to let the PC see the consequences of that action.
He goes on to say "I hope to someday assemble a post mortem/dissertation on what we did and how we did it, but I may need to wait 'till our first main story is finished - we have a long way to go!" So we have confirmation that defeating the Armada and reaching El Dorado will not be the end of our Pirating adventures. Good to know!
That's all for now. If I can glean anymore info from what he posted, or if he posts anything else, I'll say so here!