By far the best improvement in my eyes would be more interactive! NPCs.
Other NPC Pirates / Merchants / Soldiers, on land and on sea. With some bigger, populated islands / towns.
There could be differnt difficulties for NPC ships. Marine Ships could be friendly at first and only attack if players have a bounty on their head. Trading Quests for the merchant alliance, where you have to bring goods from one town to the other. This would bring more variety and support differnt playstyles.
Further more I'd really like to see an island like Tortuga. A pirate capitol, where there's still pvp enabled, but guards will attack aggressive players, so they HAVE to behave in some sort... :) To fill it with life you could implement differnt social mini games like card games and other tavern activities. Maybe special vendors, that sell things you could only buy in this town, so players are forced to go there.
Edit:
PLEASE change the aim of npc's (skeletons). Their 100 % accuracy is really annoying! Especialy if you heal yourself, run and jump around they could at least miss SOME shots. :D
