@garnetdivine
@red0demon0 is right about the developers changing the spawns and limiting the skelly sloop as the only one to spawn directly on a player sloop. Unfortunately he's also correct when assuming there could be a bug allowing skelleons to still spawn on sloops. They made the change a long time ago but sloops still randomly but rarely have skelleons spawn on them.
Saying there is literally nothing a sloop can do against a skelleon is just flat out wrong though. I have soloed hundreds of skelleons on a sloop. Sometimes two at a time. Don't get me wrong, they are tough, but definitely manageable weather you want to fight or run.
You say you used islands to get them away from you. That works, but if it didn't in your case than you didn't put enough distance between them and you. Don't just use the island, take advantage of the wind and put as much space between your ships as fast as you can. This is done more easily depending on how much water the skelleon has in it. The more water, the slower it moves. Doing some damage to the bottom deck will fill it some and slow it down.
You say you boarded them. Also a great tactic. Pressure on the skeletons up top will keep them from shooting your ship, while pressure on the skeletons below can keep them from repairing holes. You can put a hole in the front of the skelleon on the bottom deck, and a pirate that boarded can guard it very effectively since that hole will be located in the ship's brig, making it very easy to defend from repairs.
Keep in mind that skeletons don't have buckets. Once water gets on their ship, it can't be removed unless a player removes it. Ramming them (or them ramming you) makes holes, which take on water, and every drop adds up. Ram them and keep your ships together side by side, don't repair the hole in your ship, and continually bucket water from your ship to theirs. They will sink, and the best part is their cannons can't hit you.
Chest of sorrow can be an easy way to take one out as well.
Use firebombs on their cannons to kill the ones trying to shoot, and then hit your cannon shots below the waterline until they go down. Some green cursed cannonballs work really well since they essentially stun the skeletons preventing them from any activity, and of course peaceballs and ballistballs are amazing when timed right.
The seas are dangerous and unforgiving. It isn't just pirates you have to worry about. Skelleons are meant to be a challenge or they wouldn't be fun, just annoying. Even though you ended up losing the battle, I hope you at least learned something that will help you in your next encounter. Try not to think about skeleton galleons versus player sloops as something that needs to be changed. Instead try to think about what you could change with your tactics to overcome them. I guarantee it will be much more satisfying sinking a skelleon after they have been such a problem for you.