Advice for improving the final boss:
1: Make it immune to boarding. It's simply too easy otherwise. If you don't want to do that, make it VERY resistant.
2: Give it sails and a crew like every other ship in the game
3: Give it backup, like 2 mini ghost ships
4: INCREASE ITS HEALTH! 2 blasts from a high level ship with dynamite can deal 3,000 damage. It should have more along the lines of 30,000.
I was quite disappointed by the difficulty level of that boss.
@GhoullyX It is very difficult, but if you think that having max upgrades will let you win every level, think again. Try using strategy. For instance the Big Shark can shoot around corners, which can give you the edge, but the Fish Bone deals more damage.
I wish that there was an ending where if you had a "this is a square" sign in your inventory and you put it on the cube, you would be able to understand the concept of a square with depth and get a slightly less bizarre ending.