I don't have the whole idea crafted yet, but would love to throw it out there to the creative minds that can add to it.
When at sea and attacking a pirate ship, if you've got them down to maybe 20%, allow an option to cross the plank and either kill the crew and captain and loot the ship (giving ship comms and gold) or kill the captain and subdue the crew, making them temporarily loyal to you and the ship under your command. This would give you a temporary ship that you lose as soon as you get off.
I'm thinking this temp ship wouldn't be able to dock at any conventional harbours, but open up a couple new ones only accessible by this way.
Also thinking the opposite could be true, where if you're about to sink, you get a prompt to try and bail to their ship and join the crew, opening up a new area only accessible by this way. (some mutual and some exclusive areas between captaining and crewing denizen ship)
Feel free to do a little snippy snip or duct taping to this idea.