One awsome thing would be to have a whole menu system dedicated to creating a custom boss.
When you go to the menu, you'd be able to choose how big it is. Then you could select the parts of the body. Here's the cool thing: There would be a click and drag side screen, allowing you to construct the boss, and animate the way it moves(EX: Hop, Slither, Walk, Run, etc...), and select the tile that you want to be it's weak point, and the weapon of choice to use against it. You would also be able to type in a HP #. Then you could name it, and save it to the enemy list, OR have an enemy menu dedicated to your custom bosses. Then, whenever you want to use it, you could just go to the enemy list, and set it. There could also be a flag named: "Custom Boss #" to set where it'll be when you enter the room.