First off, Admin, thank you for asking. Many games at this stage forget about the playerbase.
1: Crafting is a grind and anyone and everyone can be a level 50 shipwright as long as they grind it out.
Suggestion: 1) Add crafting missions for leveling. Ie. We must defend the town. Go craft 30 iron ingots for canons, and get exp and $. Go craft 10 light carriages for the canons to sit on, and get exp and $.
Suggestion: 2) require buildings to craft corresponding items. Just like a shipyard is needed to build ships. A foundry/blacksmith should be needed for casting. A woodshop for working with wood and so one.
Suggestion: 3) craftable cannons..... I oh God please! Allow for focus to change stats. Ie. Focus on range or durability or weight or stopping power. Please, I really want craftable cannons!
This will cause few things. More choices in crafting (pick your focus) , fewer first rates for sale(I believe you said you wanted to reduce that), and cause clans to work amongst them self to produce a ship.
2: Finding a ship for sale. You have to either know someone that can make it or sail from port to port to find it. Yes it's realistic but it's a slow laborious process.
Suggestion: Allow players to see all ships for sale in their nations ports and freetowns. They will still need to sail to the location of the ship to buy it, however they know what they are getting and don't go crazy trying to find a ship. This would also tie in nicely with my above suggestions.
3: AI actions. I'm at war with a nation and I can sail right us to their AI fleet and nothing happens.
Suggestion: 1) AI fleets should attack an at war nation's ship whenever it gets within a given range.
Suggestion 2) for balancing and to allow smuggling, you would have to reduce the number of ai fleets or ensure the range is smaller.
4: Pirates. I don't believe they should be a traditional nation. The it really kills the realism.
Suggestion 1) set pirates up to be more of a mercenary for hire. Allow them to get letter of Marque from nations and receive exp and $. 1 letter per captain Ie. The US gives out letters of masque to hunt Spanish ships.
Suggestion 2) if a captain has a letter of Marque from a nation he can not attack that nation with out losing the letter. Balancing may be needed.
Suggestion 3) pirates can only have groups of 3. It was fairly rare for pirates to have large fleets. This will also force pirates to start sailing as pirates and focus on smaller faster ships attacking traders rather then sol. Balancing may be needed.
5: Wind. It's to predictable.
Suggestion: 1) make it change direction sporadicly but not all at once. Ie. Don't go blowing east to west 1 minute then west to east the next. As a matter of fact, use the current system, just have it go the other way once in a while. ????
Suggestion: 2) add in small changes in wind speed that impact ship speed.