The main purpose of this suggestion is to boost the popularity and usefulness of the smaller ships and give more life to the shallow parts of the map.
So, I would like to suggest the creation of Trading outposts/ Smuggler-privateer havens.
What are they?
They are small ports/coves which will spawn in pre-determined locations like in Port Royale 2. They will only be accesible by 6th and 7th rate ships(Requin excluded). They will be destructable by enemies using the normal PB mechanics. Defences can be built up to a tower or two. A grace period of one or two days could be given after its establishment where nobody else but the clan and its friends can enter, to allow the build up of defences since everything will be at stake. Timers will apply here too.
Map from Port Royale 2. Spawnable towns marked with red
How can you get them?
They can be created or gifted by the viceroy of the Nation, after a clan has proven its worth to the nation and has captured a number of enemy ports and earned enough victory marks. Could be tied to strictly shallow port. Upkeep could be (shallow) victory marks or settlers/special crew that drops or it could be crafted in normal ports.
What can be their uses?
First of all they could be specialised to either Privateer-Smuggler havens or simple Trading Outposts, or could be combined all to one.
They consume special smuggled goods that drop in normal ports(possibly random ports) and can't be sold anywhere else at a decent price. Captains carrying those goods could be flagged like when a player carries a chest now.
Specialised small shipyards that could provide refits or special bonuses to 6-7th rates. Could possibly stretch it to shallow 5th rates.
Can create its own special goods in small numbers to be sold in the rest of the ports
Privateer tavern(building) that allows you hire experienced privateers(allows to craft special boarding mods)
They get increased raiding range which allows you to pull raiding missions for ports that are further and slightly raise the loot
They consume very limited numbers of goods of the region they are in