I like the idea of ship upgrades that assist the way that you play, but only at the cost of being unable to use any the other upgrades, so you only get 1, for example:
1 - Bow Chase Gun - For the PVP player who enjoy the thrill of the chase, a front mounted cannon.
2 - Stern Chase Gun - For players who want to repel a PVP player whilst on the run, a rear mounted cannon.
3 - Side Netting - For the adventurous player on the move, side nets that collect floating barrels in the water, collecting the resources into the currently unusable lower deck barrels for players to use while on the move.
4 - Naval Ram - For the brave and the bold, a Naval Ram that prevents forward damage from ramming attacks while increasing damage to ships rammed.
5 - Increased Storage - For those in the long haul, increased storage supplies to store more cannon balls, wooden planks and bananas.
6 - Secure holdings - For those who need some extra security, adds a crew locked compartment that prevents non crew members from obtaining loot, forcing opposing ships to sink the vessel to gain your items.
7 - Forward Mounted Spear Gun - A weapon that attaches itself to a ship, preventing it from gaining ground while allowing the shooter to reel in the vessel. Takes considerable time to load and for ships hit to hold F to remove the hook.
8 - Swivel Guns - Smaller cannons that have limited damage against ships but are deadly to players and skeletons. Great for clearing out smaller PVE enemies without wasting cannonballs.
9 - Heavy Munitions - Advanced weapon supplies giving the ships crew a heavier version of the blunderbuss that consumes 2 weapons slots and consumes cannon balls, providing players boarding ships the option to inflict damage to a ship without relying on their own to open fire. Would also have the option for small scale hand grenades that consume 1 weapon slot.
10 - Captains Parrot - A parrot that can be released after anchoring to find random / hidden items on an island. Useful for finding a players hidden chest, random chest/trinket/bottle spawns.
11 - Fewer supplies - Decreased supplies on board a vessel but gives the vessel increased handling and speed.