It goes without saying but SoT is a very watery based game and yet so little depends on it.
Rain
More smaller rainfall should occurs without the danger of the storm to keep you busy on the sea. (this is linked to the other suggestions)
Weapons
An intro to some water based weapons to that would actually work underwater; harpoon, trident.
If the player is under water or in the rain, there could be a chance your weapons jam causing you to empty your gun and reload.
Soggy clothes
Like the merchant cloth, clothes get wet.
Add a small animation to clothes when in rain that darkens your outfit making you look from wet to soaked.
Maybe a decrease to sprint speed whilst soaked.
Rust
If the gold skeletons rust, why don't their skulls, or the gold trinkets.
This feature would have to be slow but could add tension to collecting Loot.
A rusty item could cost less meaning all the more haste is needed when looking for Loot on the seas.
Umbrellas
Small parasols that spawn like Loot on islands.
Pick it up and avoid getting Soggy and attach it to your cloth cargo to shelter it instead of waiting for the rain to pass.
This could also be used for gold looking skulls and trinkets
Rum Bottles
A common way to move rum in SoT is to jump into water. SoT isn't a realistic game but I expected the bottles to float up when a player carrying rum submerge beneath a body of water.
Would be a fun nuisance to the somewhat stale cargo runs, collecting your rum like messages in a bottle after sinking a skele ship
