1. Add a tab in port so you can see who is currently at that port as well and what ship they are crewing. (If you dock at a port in real life, you're going to see other ships.) This will help prevent pathetic carebear gank squads from sitting in port for hours waiting for solo players to leave. You will now know that they're there and you can leave at your own risk. Also, your name remains on the port list for a minute after you un-dock, this allows proper time to drop canvas and if you ARE chased you can give a proper chase.
2. Remove invisibility, I don't even know why this is a thing. The other choice would be to put a timer on port re-entry so you have to go visible before re-docking.
3. Trading ships should be allowed an extended yardarm upgrade and an extra canvas upgrade, allowing them to run at 130% sails in battle. This forces enemies to carry those same upgrades, fore-going their normal upgrades, if they want to go out capping traders. Even if the increased speed came with a decrease in maneuverability it'd be worth it. (I'm aware of copper plating and speed trim, those are for the hull, we need something for the sails.)
4. Battle Timers should not exist whatsoever, you can't get from any one port to another within 2 minutes, why would reinforcements be limited to a window of that time? Ridiculous. Engagements should remain open to either nationality fighting until they are resolved by sinking, capturing, escaping, etc. This would make grinding mission more enjoyable as well because you have the option to sail around helping new people with missions without the requirement of grouping.
5. The "pick-a-side" mechanic is retarded. If the United States and Pirates are in a battle, the Spanish should not be able to engage under flags of Piracy or the United States. (until diplomacy is worked into game) (In this respect diplomacy shouldn't be open to pirates.) This would solve mission ganking issues from all factions, except pirate of coarse.
6. Pirates should have to defect from a nation, not be their own nation. (Which means I agree with pirates not being able to port cap and no nation chat)
7. Pirates should be able to sail under letters of marque, improving their relations with a certain nation to the point where national players can't attack them. Being a Pirate they can abandon these letters at anytime and re-engage piracy against that nation. Their mission system should be based off these letters (sack ships or raid cities of nearby nations for rewards).
8. All Ships should be renamed for the type and class ship they are, not real ships that existed. Seeing Dutch and French players in a ship named Constitution isn't right.
9. To go with #8, You should be able to name your ship.
10. Contracts from other nations should be removed from ports once you've capture them.
11. NO OUTPOSTS IN FREEPORTS. This prevents nations from bouncing in behind enemy lines and forming massive gank squads where waters should be relatively safe. I enjoy PvP a lot, but I shouldn't have to worry about getting port ganked around freeports deep within my nations lines. If you want to harass your enemy behind their lines, sail there from your closest nations port. 12. You should be able to hire AI trading escorts with no level cap. The higher rank you are, the better the escorts you can hire. (Incentive for people to put more time into the game) 13. Teleport function should be disabled for ports that have been captured be another nation. If you have production buildings there, recap the port.
14. You should be able to hire a crew from your outposts to sail your ships to another outpost of yours.
15. Why does every AI ship carry marines? Stupid
I had more but I can't think of them at the moment.