not saying this in a mean way.... but just uninstall? hear me out...
you seem to be similar to myself. you enjoy the pve element of the game. you dislike pvp. you login to complete some tasks but every time you leave an island you get unwanted pve spawns that are just adding speed bumps to your progress. easyish to deal with MOST of the time... but every so often the game will decided to spawn a random skeleton galleon on a solo sloop (no not part of the fleet event. just either a low chance of happening OR a bug from when skeleton galleons were the only skeleton ship? the addition of the smuggler skeleton ships full of useless loot no one wants. if you are working on skeleton ship commendation after getting pirate legend this skeleton ship frequency is kind of amazing. but as you said you play safer seas pirate legend is out of reach.
if they are going to unlock everything in safer seas, which they are dead set on not making it better, then the bottom line is we arent the type of player they want in their game. which i guess is fine if they dont like to keep more potential cash shop customers around... they have lost millions already because of it. but their vision for the game is stronger than their drive for profit.. honestly commendable in a way? or they dont realize how much they are hurting themselves with this mentality.
sadly with only 1 ship on the server the pve elements only have 1 choice for attacking so you get ALL the spawns. the 2 skeleton ship issue might be lack of experience on your part? if you see a ship cloud up in the sky that is a world even where you fight waves of skeleton ships so when that cloud is up, avoid the center of the map.
i love the art of this game, i love the world, the pve. the fact servers still run like garbage hurts the experience. their focus the wrong things and going full OCD mode on stuff no one actually cares about that has more a negative impact on player moral than anything else. IE the doubloon issue. literally no one cared. add the items so we finally had something to spend the money on. instead they swing the problem in the total opposite direction.... the screw up the reset and decide they should punish the few people who managed to keep their doubloons and could buy all the things right away.
as theres literally no progression aside from gold farming in safer seas and gold is useless af.... lets just go find something better to play?