Thinking to other pirate type games I've played over the years and just the nature of piracy at all, some thoughts. Since NPC ships have now been established as a thing Rare can do, another great map event would be a treasure fleet. Several NPC escorts (Brigantines would be good) with a treasure laden Galleon in the center. The loot should be primarily focused on the Merchant Alliance as this is the only faction that doesn't have a major event good for XP/loot. Forts = GH and OOS with minor MA, same goes for the Skeleton ships.
Alternatively, since they are introducing a new type of Merchant Alliance quest and items (bring items from port A to port B), the player has effectively become the treasure fleet. With the use of the Alliance system, other players can now form the escorts and now appear as a convoy on the map for all to see. If the players achieve their goal, the spoils are shared across the alliance as per usual, if they are sunk, to the victor go the spoils. Perhaps a reward bonus based on delivery time? Maybe also have varying levels of escort quests. You could bring a couple of chickens for a relatively safe and easy reward vs bring a ton of expensive items which will incur more risk but better reward.
An additional point on MA quests. It would be great if they didn't expire outright. Sure, have a preferred time of delivery but if you miss that, you just get less loot but can still deliver as requested.
I haven't fully read up on the new MA things to come so if all this is already in the works i'll be excited. If not, some things for Rare to consider hopefully!
