I think there should be a boat destruction system, where, depending on what parts of the boat are destroyed, some things may happen, if you are hit in the sails, you are slowed down, if you are hit in the back, you lose the ability to steer, if you are hit in the nose, you are immobilized, and maybe you could repair those parts to prevent your boat from sinking (I dunno, I'm thinking about Blackwake's boat damage system right now), some other ideas would be each boat having its own crew, like, boat 1 has some MK1 Swords to board your ship, and they are being aggressive, while boat 2 has some MK1 Archers, that are playing more defensively and trying to behead you with their arrows, also, what if boats had cannons that you could shoot? Imagine fighting the Orcaneer with that, or just sinking enemy boats... oh, and you'd be able to board boats cuz y not :3, amirite?
Also, maybe a flintlock or musket or blunderbuss shoud be added as ranged weapons that are like shotguns, and they would fit well with 1 energy for 1 shot, as those weapons took about the entirety of the King Kong movie to reload.
Another reason why boarding boats should be a thing would be so I could "This is Sparta!" everyone out of their boats. Also, alongside the rafts and boats, what about some BIG flagships with minibosses such as Spidertron and MK3 Hammers/Archers, or maybe even Cyclops or Anubises!