I believe diplomacy mechanisms are the most important to address at this time. The other topics are also important, and i hope the devs can resolve them in future updates.
I am a pvp player. I have not done many pve battles and have leveled mostly in pvp battles. Port battles are a great XP and $$$ source, even after the crew update. The heart and soul of this games long term players is pvp.
I do see one fundamental problem with the current game. That is, the over abundance of ports, and the lack of any real payer ownership or responsibility once capturing a port. I believe the number of ports should increase as the server pop increases. Here is how you do it: You have a map with just capital cities and nearby ports in a no pvp safe zone. These ports have limited resource potential, mostly food and wood. Land masses outside of the capital land will have different sets of resource fertility. Player clans can sail out to these lands and explore or survey the land. They can then found a city an that city could allow resource buildings based on the fertility. A city costs upkeep, for things like port defenses, needs to be stocked by the clan with munitions, cost of hiring Ai fleets to patrol the rout between the city and another selected city. Clans could make the city their home city. They could found additional satellite cities etc... All based on if they can afford upkeep. Trader clans could create trade empires this way, pvp clans could pvp in port battles or defend a friendly clans city, etc. Clans could go to the capital and buy a letter permitting them to go to war with another clan and set a victory condition, eg. Capture x port, sink x gold worth of ships, etc. An honor system would also need to be implemented. You get honor for sinking enemy nation ships, lose honor for sinking your nations ships. If your honor goes too negative, you get the mark of a pirate and anyone can sink you. Clans can decide if they want pirate players to enter their city, forcing those who enjoy being pirate to clan up and found pirate cities. Pirates would still retain the nationality of the nation they started as, and could pay gold to purchase a difficult mission to return to 0 honor. Pirates would not be a nation. Pirate clans could exact ransom on neighbors and pvp clans could hunt enemies and pirates and vice versa. Having each clan create its own ecosystem of cities will allow them to specialize, and trade would be vital. Alliances could be forged with clans, not a one dimensional nation to nation alliance that can't be enforced. Ally clans would have green names, neutral gray, and enemy red. Resource output in the buildings you could purchase in cities would be tied to the lands fertility. Ports can be upgraded to different levels, 1-10. If an enemy wins a port battle, they can keep the port but it loses half its levels, or they can pillage it for loot and it loses a third of its levels. A level one port can be demolished. Free ports would still be a thing, anyone could use free ports, and they would be pre exiting like the current ones. Clans could set up free ports in their own ports by having the clan leader select the preferences in a port management screen.
This idea could be expanded on and I hope the war and peace update is a move in this direction.