Mechanics of Targeting enemies is wonky, when pressing space, all enemies are killed instead of the one being targeted, if you have an object to represent a weapon you might be able to use that alongside collisions to test what enemy is hit. instead of a critical hit while in water(unsure because of the inconsistent attack mechanic) I might argue you want to make a mechanic where you make a leap attack out of water that deals damage/kills enemies that are hit, this allows for multiple uses like leaping over a boat, killing the enemy on top and landing in water again, leap on top of a larger ship while killing the enemy you land on or just simple movement options.
with this you might also be able to change the location the game takes place in, if you set it in a larger river with multiple feudal Japanese boats and ships you will have a larger area to play around in and the player will be able to choose his own path.
backstory in this case can be that you have to deal with the pirates travelling trough the river and disrespecting the holy site of the water spirit
I would also implement a speed boost in water to further reinforce the point that water is where you are strongest