Perhaps in the future when the game gets a bit more advanced you could add a gravity system to the raft, where if you build a couple of trees on the edge of the raft it could capsize.and if you continuously add more and more weight in the center without having the size to support it, the raft would start to sink. and in addition perhaps more refined resources and advanced structures could be added and more advanced stations to produce and refine the resources, perhaps a mulcher to turn excess biological matter (rotting food, fish meat, fruit, plant parts, etc) into fertilizer to keep growing more plants so that you have to put more effort into farming than just "build pot, click seeds on it, profit"
and with the idea of refined resources, perhaps cotton could be added and a weaving station to turn it into cloth which could be used to construct ballasts to hold up your raft and provide more buoyancy letting you put more things on your raft. defenses to protect your raft and advanced structures from additional threats. a soil fertility system where certain plants need certain fertility levels to survive. and each plant harvested removes fertility.
More enemies and disasters, perhaps even include mythical sea monsters in the future. such as fish people that invade your raft. pirate raids, a disaster where temporarily there will be a big pack of sharks around your raft, about 25 - 30 that will leave after a few days but if a higher difficulty is picked there is a chance some of them would stay behind permanently until killed. Typhoons and hurricanes that toss things about, rip your raft apart, and if set to a higher difficulty. even pull the player off the raft and into the ocean.
More weapons and reinforcement options to deal with these disasters. perhaps a way to harvest sulfur and nitre from rotting meat, and charcoal from fires in order to forge archaic gunpowder weaponry that must be unequipped before entering the water or else it will be ruined and can't be used for several days straight for the water to dry. crossbows and metal reinforcement options that increase weight and armor. and ways to armor yourself
A food spoilage system that doesn't just ruin your food and is actually required to get certain items and equipment. and ways to preserve food for storage such as salting, smoking. and turning it into pemmican (essentially balls of smoked dried meat, melted fat, and sometimes dried fruit).
Rare shipwrecks that can float by your raft that you can get important equipment and items from.. and an expensive way to tie them to your raft so you can thoroughly harvest everything they have to offer. such as irreplaceable mechanical items and equipment like dive suits. proper guns that get permanently ruined in water oxygen tanks, harpoons and harpoon guns. possibly wiring and diesel engines as a way to generate power for your raft that are very heavy and get ruined permanently when they get flooded because the raft sunk, or because they were not given proper shelter during a storm and where ruined that way. saw, blow torches, and advanced tools that are required to properly disassemble diesel engines in order to use the parts to repair other ones and hook up wiring throughout your raft. plastics that you can use to storm proof rooms. and when you are finally done with the boat you have tied to your raft. harvest all the delicious metal with a saw or torch. or else it must be let go.
Threats and traps that make shipwrecks chancey encounters rather than floating resource piles. (something had to take away the people) such as mermen (fish people) that have lain a nest on them. rat and carnivorous crab infestations. that can either overpower you and ruin your life on the raft and devour every scrap of food on board. the crew of the vessel that ran out of food, went insane, and turned cannibalistic. exposed wiring and jagged shards of metal that can hurt and kill you that you must either wait to run out of power, cut away, or find a way around to capture the valuable fuel that is powering the wiring.
And last, but not least. Quality of life improvements, plenty of bug fixes, better AI, and even possibly graphical improvements.