I had a few ideas for things to do in the game.
Escort ship missions. This brings several things to the table. Crew Skill, a real reason to PvP outside of just sinking someone because you're bored and hopefully a good payout. On the flip side, as a PvP player, you know you have to battle the two ships, (The player crew) and the NPC Crew (Think Skelly ship). But again the payout would have to be worth it.
With the captaincy update, you can introduce bounties tied to the ship name / Captain. As a pirate crew sinks ships tied to certain factions, they get bounties placed on them. Turn in the ships log to the appropriate faction and claim your reward. Again make it worth it. 1,000 gold isn't worth it. How would you know if there is a bounty on your sever? Every outpost has a bounty board. Any Captain on your server with a bounty will be listed. Then it's up to you to find them.
I really don't like the built in ESP where the game shows you people on the map. It's a bit lazy IMO. You have a spyglass for a reason, use it. Which would make bounty hunting a great cat and mouse game. Since the spyglass shows the ship name if they are a captain.
"But then players would just not use a captained ship and use a base game ship" I hear you say. Then make being a Captain have more in game benefits, like access to captain only missions, just like Pirate legend. Or you have to be a Captain to turn in bounties. Saving up for a ship isn't that hard. I don't think it would too hard to had these features to the game.
Thoughts?
