I'd like to see the faction system get a bit more depth. Like the ability to raise the flag of a particular faction. While you have that faction's flag raised, you would gain extra rep with that faction, but you lose rep and could eventually become barred from raising the flag for that faction for attacking other ships also raising that flag. Perhaps there could be more lucrative mission variants, which involve constantly having valuables on your ship throughout. Then you would also be able to raise the black flag, which neither gains nor loses rep with factions for any actions, however, you take all loot for yourselves, giving you higher gold. So if you decide to raise the flag of a particular faction, lets you build rep faster, but it also puts a target on your ship, marking it as a target for ships of other factions or people just out there to attack other ships. It would also make the spyglass more useful as well, as it isn't hard to spot ships on the horizon without a spyglass, but is considerably harder to make out a small flag on top of their ship.
I'd also like to see outposts become some sort of a safe haven, where attacking other players is either prevented or heavily discouraged. Ship to ship combat is pretty rare because ganking them at an outpost is easier, more likely to get something out of it, and a faster turnover for rewards. Anything that makes outpost ganking less viable and open sea combat more lucrative is a good change. I'd especially like to see outposts turned into social hubs where you can actually recruit new people to your crew or split off and form a new crew, though that seems unlikely to happen. Still, the idea of a bunch of people just hanging out in a tavern when someone comes in with a treasure map asking for those who would sail with him on this adventure is a something I would love to see.
Furthermore, I'd like to see more gadgets/weapons, and greater specialization. Not necessarily anything new to unlock, but more item slots with multiple options like the weapon slots. Perhaps even some kind of class/title system that improves certain actions and can be changed at an outpost. It could work by bragging to the barkeep about your exploits, and the things you brag about turn into actual bonuses. It could be three sets of three choices: a combat focus, a bonus to manning the ship, and a fun one with no real gameplay impact. So an example could be something like "no one's a better aim than me, manning sails than me, and musician than me" for less spread with guns, faster adjusting of the sails, and plays alternate versions of the songs on instruments, respectively.
Lastly, one item I would love to see in this game is a grappling hook. It would essentially be used to pull the ship towards things. You could latch onto other ships and pull them into boarding range, or you could use it to pull into a port and properly dock .
