As ideas...
-Add more types of food (like carrots, radishes..) but more difficult to obtain. (Cotton for make cloths also)
-A day and night cycle, what means to add a bed
-More types of fish, ones friendly, other agressive
-Food degradation. The food can rot after a while
-Temperature system
-Diseases, by drinking dirty water, by eating food in poor condition (food degradation), sunstroke during the day, hypothermia at night (add bonfires, which will play an important role here to maintain the temperature)
-Shark Algorithm: When killing the main shark, increase the number of sharks that spawn at the same time, progressively, or make the sharks harder to kill. In Hard mode, at the beggining would appear 2 sharks. (or something like that)
-Improve the wood floors walls etc with metal, making them more resistant to attacks
-Weather system, rain to collect for drinking, thunderstorms + rough seas (which can break the ends of the base), etc (That includes natural disasters like hurricanes, Tsunamis...
-Add more items and weapons! Fishnets, Bows for hunting, etc
-Defend the base with spikes, torches to keep sharks away
-Fall Damage
-You need blueprints to make complicate buildings/Items
-Cloths and armor, with leather and metal
-More buildings
-Smeltery for making better weapons or improve your actual ones
-Floats that must be placed while you expand the base (or the base will sink, but thats a hardcore idea)
-Goose barnacles glued to the base which you can take off and cook for eat (Why not?)
-Maybe... brocken ships near the base with loot
I dont have more ideas right now.. If I think anything else, I'll comment it below! (PD Sorry if you dont understand something i dont speak a lot of english)