The main issues I have in the dark sea (which you have mostly covered here) are:
Acid waves. They do not need to do that much damage. Plasma waves seemed to have gotten nerfed and no longer deal a ridiculous amount of damage so acid ones should as well. I know it makes sense lorewise but it also is painful to deal with
Waves dragging you off the ship. The already have their thing that they do to be a threat, which is damaging your ship. This is mostly fair, and it wouldn’t feel like it is too safe if they can no longer carry you away.
The forests. Very nice to look at, but outside of literally the first time you encounter them, you do not want them to be spawning ever.
That one type of island where it’s just a bunch of cubes made of stone that are really annoying to climb and you get barely anything from it.
Atlantean ships. I do not want to have a very tanky ship chasing me for ages shooting mortars at me.
Giant krakens. Why can these ones hit you while you are on your ship and just kill you almost instantly? It’s pretty unfair and it’s happened quite a few times now.
The tornadoes (especially poison or shadow tornadoes). They show up at the worst timing.
The little puddles that give poison. The larger bodies of water that give it are fine, but stepping in the puddles is something that happens quite often, and only in certain biomes.
The little smaller rocks and structures that are in the water surrounding the actual islands. They are good on paper because they help you find islands, but you don’t actually need them since you can sense islands and instead these things just always end up directly in front of you and you crash into them the moment you do anything that isn’t looking where you are going.
The fact that I searched about 6 very large islands for a cooking pot and did not find any, nor did I find a cauldron. I normally don’t have any issues with finding them so it was probably a bug but still annoying.
However, there are also things I find to be less of an issue than most people such as:
The lightning. Yeah it can be annoying when it hits me, but mostly it’s just a bit funny. It has also helped me out in numerous occasions, such as by killing most of the atlanteans on a ship or damaging a dragon that I’m fighting.
Gear becoming damaged. I have literally never had this happen to me and I’ve fought quite a few larger dragons, and taken quite a few hits from them as well. That doesn’t mean I think it’s a good feature, just that I haven’t had an issue with it.
Managing supplies. This is probably just because of my ship being tanky but I really don’t have much of an issue with taking much damage. I can roam around in the far reaches for literal hours without having to use cargo for supplies.
Anyway these are the parts that I personally have stronger opinions on, so hopefully they will be useful