For me skeleton ships are currently the most annoying thing in this game, even more so than other player crews.
You can get out of the ink circle of a kraken, and it'll just sit there and go away after a while.
A megalodon will go away if you get near any land mass.
Both of them also hit very slowly. Skeleton crews on the other hand have a skeleton for every single interactable object on their ship, and they respawn ten times as fast as players. Skeleton ships are also always galleons, so whatever crew amount or ship you have, you always face the max firepower that is possible in the game.
I always dread sailing out of an outpost after a resupply and hearing the slow base drop and the action music kick in. Not because I'm scared they'll sink me, but because it's such an inconvenience. I've learnt that if you sail right back to an island and wait there for a few minutes, then sail out, they will not spawn and the music will fade out (though sometimes I just get 2 ships in a row, and end up fighting the second).
In my entire time playing this game (and I'm almost pirate legend with no level purchases), I have never been able to "escape" a skeleton ship. They keep following me at 3 times the speed of a normal galleon until either I or they sink.