I guess the reason you're doing it is to have fun writing new stories each time you sail, the excitement of a fantasy pirate adventure, whatever. The combination of different factors leads to fun and memorable moments. Earlier today, I pulled up to Morrow's Peak in my solo slooo to start cashing out (GH voyage, plus some shipwrecks, random stuff from beaches, and a meg) when the volcano erupted. I started to move away, but having got stuck against the dock for a moment had several fires to fight and the water coming into my ship was boiling! At one point I got hit by a volcano rock and found myself on the Ferry of the Damned. When I got back, I was being attacked by a skelly sloop! It was a fun battle as I fought them off and brought the fires under control at the same time. Eventually I sunk them and fully repaired my ship, and retrieved the skelly ship loot, taking me from emissary grade 4 to grade 5. I went and sold, making about 70k gold, but more importantly a fun story that I won't forget any time soon!
As others have said, everyone having the same load-out without persistent power progression is a core aspect of gameplay, that actually is quite positive.
As others have addressed that, though, I definitely hear you with regards to how krakens and skelly ships feel when you're new! Especially if you mainly play solo, as I do. However, experience and knowing what to do will help! With the kraken, keep firing your cannons at its tentacles; once you've defeated 3-4 in a sloop, it'll leave. The main thing is to try not to get sucked up – if you see a tentacle mouth come close to the ship with wind lines, get below deck for a while. Like megs, krakens scale in difficulty according to the ship they attack. With a little experience, a sloop kraken is easy to defeat solo.
For skeleton sloops, you just want to rain cannonballs and firebombs on them until they sinks. Look out for cursed cannonballs, and above all try not to get knocked off. Rate of fire is your friend; it keeps the holes open and skeletons can't bail. So it's a case of practising marksmanship. Prioritise bailing out water over repairing holes, unless you've taken a lot of hits. If you can get yourself stuck up against the skelly ship, you can bail water from your hull into theirs. Skeleton galleons are a bit more difficult, at least when solo, but they shouldn't spawn against player sloops* and won't attack you if you give them a wide berth, so that advice can maybe wait.
If you want to fight a meg, just come to a stop, load cannons and shoot it whenever it's in your firing arc. When it's not in your cannon arc, shoot it with your flintlock or eye of reach. Try not to get knocked off. Earn good loot as a result.
As far as the having fun goes, I can promise you that working out how to take down those PvE encounters will be a brilliant feeling when you start to get there! After 30 skelly ship sinks, watching them slip beneath the waves still doesn't get old. The same is actually true of PvP, although I'm still very much learning how to do that myself.
Hope some of this helps! It's all a matter of experience, and learning when to prioritise attack and when to prioritise repairs. Good luck, pirate!
*Occasionally you can get very unlucky and be passing a spawn point for the 'roaming' type of skeleton galleon when one appears, and immediately aggros on you. It's not spawning on you strictly speaking, though, and this is a rare occurrence.