There are a few things I find annoying, and I will suggest some solutions to them, as well.
1. Rotating the whole ship you're on becomes more difficult the bigger the ship gets. Maybe have a pedal-powered wooden gyroscope, used to rotate the ship, which also increases the weight of the ship. Or maybe have another tier of propulsion in between paddling and steam engine. A good example would be a pedal-powered propeller, which would need some processed wood, rope and tar, and would give as much power as the paddling plus a third/quarter of the difference between paddling and a steam engine.
2. Side-rafts. Basically, smaller rafts which one can use for scouting, for moving around without moving the whole base, (with a risk of getting lost), and could even have a limited range. For example having multiple tiers of relay towers needed to be built on the main raft and another relay tower on the side-rafts, which would dictate the distance. The higher the tier, the taller the tower, and the more expensive in terms of components. Might also overlap with the island watching tower. The second tier would be two blocks tall and use more wood and rope, and some tar, the third tier a piece of glass (for optical telescope telegraph), the fourth tier would 3-blocks-tall and require even more glass, and the fourth tier would also need gears to fine-tune the zoom and focus on the tower.
3. Another option for the priority list, defending the raft against attackers other than humanoid monsters (i.e. seagulls, sharks, tentacle monster).
4. Bombs/grenades. That way, we could more easily deal with AI which are stuck, and even avoid having to fight, by setting a trap and baiting the people to come after you, or by setting a trap and timer-detonating it (i.e. after you place it, you have 3 seconds to get away from the bomb, before it explodes). Different tiers would have different ranges (i.e. one-block effect for the first tier, 3x3 for the second tier and 5x5 for the third tier. Also, the damage could be calculated from the outside in, incrementally. The first tier bomb would have the same damage on that one block as would the 3x3 and 5x5 on their respective outer rings. And the 5x5 would have the same damage on it's inner ring as would the center block of the 3x3 have.
5. Repair All does not, in fact, fix all. It should fix buildings, floors and walls. Even holding the shift/ctrl/alt keys when pressing the button doesn't do that. I have to use the Repair button on each floor, each wall and each block, every time I want to fix my raft. I had lost quite a bit of floors and constructions because of it not working well.