The ability to Knock out NPCs and tame them or the ability to hang or behead them using the guillotine.
NPC crew can sail to player designated markers or locations avoiding obstacles the ship may encounter along the way such as land or sotd. This could be utilised by having an NPC crew mate equip a spyglass and then selecting "make lookout" from a selection wheel that could include options such as "set destination" or "target settings" for your lookout to call out if they spot a certain type of target or creature.
Remove the weird ingredients from metal forging, making metal ingots should be more like the ark mechanic put the ore in with some fuel light it and get ingots, sap and other weird ingredients just seems too weird and time consuming.
Ship mounted mortars (maybe a smaller projectile version) and puck guns
Music box that plays songs you can listen to whilst sailing.
These are just a few ideas that I thought might be cool.