really like the format, and the split between ship/captain gameplay - almost reminds me of NES blaster master
couple UX notes though -
you've gotta figure out a better way to handle the whole "which way will the cannon shoot" issue. "A" doesn't really mean anything to the player, if you equip a cannon to 'A' it's basically always a coin toss whether that means the shot is going to come out of the side you want it to or not. I do really like the inclusion of the 'broadside' type attack on a pirate ship, makes perfect sense... but you've gotta figure out a way to make it more obvious which side that shot's going to come out of.
I'm tempted to suggest something like "shot always comes out of the side closest to a valid target" but there will inevitably be situations where this isn't desired. Maybe you could allow the user to hold down the A or B buttons, to highlight the path of the shot, to be fired on button release? Maybe you could use the R-stick to point to the desired direction? I dunno. there's gotta be a way to eliminate that ambiguity.
only other small comment is it's annoying to toggle the ship whistle on and off - is there really any benefit to making it an equipable item, rather than a 'use from inventory' item? because as it stands now, it allows the absolutely untenable "oops I pressed the wrong button during a boss battle and skipped the entire window of opportunity to hit him while he's weak" turn of events, which - that shouldn't happen. as much as possible players shouldn't even be given the opportunity to hit the wrong button, you know?
anyway though, the music and graphics are so on-point, super impressive, and I wanna see more!! keep it up!