-Bounty System: Players can pay a port fee and post on a wooden bulletin board for Captains to sink a particular player for a reward. To discourage spamming the Bounty System there are a number rules that can be implemented, they have to had sunk you recently, two or more players must collectively agree to post a bounty, or make the bounty tax an expensive fee. Players who successfully sink X amount of Bounties gain a tittle, reward of some sort.
-Weather System: A randomizing weather pattern that effect ship sailing and combat capabilities is nice. A great example we see in cinema is fog banks being used to launch an surprise attack.
-Vanity Upgrades: (Real money or In-game currency) Players can buy vanity upgrades for: Ships, Ports, and Captain clothes etc...
Ships: a verity of ship figureheads, fancy lanterns, colored banners.
Ports: Guvnors can purchase a verity of street lights that line the port, upgraded docks to look more presentable, proper structures and vanity items that a "well to do port" should have. Players or guilds that own physical structures can purchase the right to hang their guild flag outside their shop.
Captain clothes: Nothing ground breaking here but a verity of hats, pants, boots, pets and so on.
-At Sea: These are visual events that again, bring the world alive. There should be whales, dolphins, sharks and all manor of sea life swimming along side or nearby for common occurrences. As for the rare moments, sea monsters and even more rare, mermaids (I know in modern time this is fictional. However at the time period this game takes place it was very much common belief that sea creatures existed. Further more this can be done in a tasteful way so that when rare events happen they look and interact in a realistic believable way). So rare that players say, "did I really just see that?".
-Crew Experience: Weather you have a crew of 30 or 300 it would be a great if you can follow the progress of your crew's experience in a log book. Each individual crew could have 10 traits rating from 1 through 100 in experience. As you sail and survive battles your crew gain experience, some faster than others and in particular areas. Players can shuffle crew around, promote and appoint them positions on the ship as Navigator, Gunner, Helmsmen, Sail master, Surgeon, Carpenter. These key leadership positions would only slightly effect the over all performance and efficiency of the ship so it won't be overpowering. But it would personalize the ships crew in a way to build a connection with gamer and the game. Of course there can be the auto manage option for the players less interested in these feature.
-Ship Building Experience: If a player/guild has been building a particular item multiple times they should be able to build a ever so slightly better quality product than someone just starting out. For instance, if you have a sail crafter and he has been stitching sails many times. He should by common sense be able to create a better product than someone brand new to that craft. To keep this from being exploited you make the advantage very slight, and the experience gained painfully slow. Other examples of ship building XP would be the wood worker or the metal fittings worker, cannon builder etc... In the long run it would be rewarding to see someone sailing a ship you or your guild built. Furthermore, your guild being known for producing top class sea worthy ships.
-Different Quality Of Material: Much like the ship building experience, this feature is sensitive to particular parts of the map. Some materials from different parts of the map are of higher quality than those from other parts. For instance, Oak from the Yucatan may have a sturdier thicker build then that of Oak from the Bahamas. What this does is gives incentive for players to explore beyond the popular location and looking for rare high quality material throughout the world. This would make that small Wood Farmer in the Yucatan competitive with the Wood Farmer in the Bahamas. Ultimately what you want is for ships to be sailing through the seas trading and transporting goods.
I hope this isn't to long winded.
-Cannonball