I have another idea, and this one i got from @TargasBR , however I wanted to bring it more in depth:
One-Session-Use Ship Upgrades.
This introduces a new Currency, and a Ship Upgrade system. These new features are limited to each session, and do not persist outside of each server.
You can now trade in supplies for Upgrade Coins. The amount of Upgrade Coins you recieve will change depending on the value of the supplies you trade.
Supply Values:
-Cannonballs: 2
-Special Cannonballs/Throwables: 3
-Cursed Cannonballs: 5
-Planks: 3
-Bait: 1
-Bananas: 1
-Coconuts: 2
-Pomegranates: 3
-Mangoes: 4
-Pineapples: 5
-Raw Meat and Fish: 1
-Cooked Meat and Fish: 2
-Raw Trophy Meat and Fish: 3
-Cooked Trophy Meat and Fish: 4
Upgrade Coins can be spent at any Shipwright to buy upgrades for your ship.
These Upgrades will improve certain parts of the ship, but if the ship goes down, they go with it. Heavily upgraded ships also have a higher chance of being attacked by Megs, Krakens, and Skeleton Ships.
Upgrades
(Low Price) Reinforcement:
A metal plating that can be applied to undamaged spots or applied over patched spots. The plating will reduce the damage to that spot, but will break depending on where it is used. You can apply planks over the plating.
For Hulls:
The Reinforcement will soak up damage 3 times, and will break afterwards
-Small Holes reduce to a Dent that doesnt flood.
-Medium Holes reduce to a Small Hole.
-Large Holes reduce to a Medium Hole.
-Explosions can still create a Large Hole.
For Masts, Capstans, and Helms:
A single Reinforcement can be used on each of these, and will soak up one hit, leaving the part underneath undamaged, but breaking in the process.
(Medium Price) Rams:
Allow you to Ram into ships dealing more damage to them and less to you.
These have a small chance to break off every time they are used, as well as when they are hit with a cannonball.
(High Price) Improved Rudder:
These allow the ship to turn a bit tighter, and are more resistant to spinning in the storm.
(Medium Price) Improved Compass:
This compass is able to go deeper into the storm without losing control, as well as having a secondary needle that points toward the nearest map marker.
(High Price) Improved Rigging:
Each one you buy is applied to a single sail, from back to front.
These make Raising, Lowering, and Angling sails go slightly faster.
(Low Price) Enchanted Bell:
When rung, this bell will glow yellow, and highlight flocks of birds in yellow for 1 second, making barrels and wrecks more noticeable on the sea.
(Medium Price) Improved Lantern:
When lit, these new lanterns will push the fog clouds away from the ship in a small radius around the lantern, allowing the crew to see a bit further while in a fogbank.
Their radius of light is also improved, meaning less dark spots on the ship.
(Low Price) Hatches and Doors:
This upgrade adds more functioning hatches/doors around the ship, and are meant to be one of the first ones you go for, due to their utility. These generate noise when opened/closed, and add:
-Functioning doors to the Captain's Quarters.
-Functioning Shutters/Curtains on the Windows
-Functioning Hatches/Doors to different sections of the ship that, when closed, all holes in the closed area stop flooding when the closed area is full. But as soon as you open the hatch, that water will drain through where the hatch opened, and the opened holes will begin flooding again. Built-up water still affects the ship's ballast and changes where it rides in the water.
Galleons can close the Top-to-Mid Hatch and the Mid-to-Bottom Hatch.
Brigs can close the Top-to-Bottom, the Map-to-Brigroom, and the Brigroom-to-Captain's Quarters.
Sloops can close the Top-to-Captain's Quarters, and the Captain's Quarters-to-Bottom
This allows players to close access to certain areas in an emergency. Have loads of holes below? Close it off until you patch the mid deck so dont sink immediately.
Conclusion
This rewards players for stocking up their ship, and gives them options to modify their ship after gathering resources. A player would be able to deck out their ship with a few things just by grabbing supplies from an outpost. Players could sacrifice their materials for temporary upgrades that expire when sunk or servers are swapped.
Another problem that has been brought to my attention is PVP.
Perhaps some upgrades would nit function during pvp, such as the Reinforcement.
What do you guys think? Thanks to @TargasBR for the inspiration.
