I was playing a game called The Hunt and I thought you should take a look at how they handle progression. It is something that is worth thinking about. They have a system where you can have multiple characters that you are leveling up, but they have something called bloodline where your overall progression is saved since you can lose a character if it dies.
What if you had a simple pirate leveling system where you could choose certain upgrades as you level up a pirate. A 1-10 system where you can choose to maybe carry an extra shot for your pistol, or extra cannons, or faster fishing, etc...
Nothing that would give too much of an advantage over a level 1 pirate vs a level 10 pirate. I would also suggest that you do not make it that hard to level up from 1 - 10, however, if you die, you lose your pirate. You keep all of your progression but that pirate is laid to rest. If you want to take this a bit further you can have several pirates that you can have in rotation so one is better a solo sailing or one is better at cooking food since that is the pirate you use for a larger crew.
You want to have several leveling options to add variety but as I mentioned nothing that would give a too much of an advantage over one pirate over the other. You could separate your leveling into branches for combat, ship functions, survivability.
Examples
1: One extra shot for the pistol, or Blunderbus
2: Can carry 5 extra cannons
3: Can carry an extra plank, or food
4: Can repair 10% faster
5: Can cook 10% faster
6: Can revive players a bit quicker
7: Can fish a bit better
8: Can raise the anchor a bit faster
9: Turn the sails a bit faster
Come up with big ideas for level 10 since losing these is risky
1: 5% extra gold for turn ins
2: Killing a level 10 Captain can maybe reward you with some extra loot should you find them
