I am a new player but I want the game to be as close to historical reality as possible while still being fun. I support Blackie's suggestions.
While there were Pirate settlements they were rare and were often in disputed / unclaimed territory or in areas unknown to the national navies. Perhaps a mechanic could be developed where pirates are able to establish secret havens that aren't visible on the map to other players. They could be discoverable and once found, the pirates would either have to relocate or risk the destruction of their haven. This could lead to a fun game of cat and mouse with national navies hunting out pirate havens only to have them pop up somewhere else. I don't know if that would work but I do not want to see the pirate faction just a renamed faction that functions exactly the same as the others.
I also don't think pirates should be building 1st and 2nd rate ships. Pirates relied on speed, cunning, and ruthlessness. I'd like to see the game find ways to allow pirates to play in a style similar to real pirates. In my opinion, the pirate faction should kind of be a prestige class that is very challenging but fun with unique game play mechanics.