Do you need that many layers ?
From my perspectivevIt seems like many user are using layers, like if it was photoshop or Gimp layers.
Layers are not an editor feature only, their intent is to be useful in the game.
How many layers do you expect to use in a game ?
Background, Sky, Sprite, foreground, ...
3, 4, or 5 ?
Surely not as many as you are currently using.
Using many layers, will eventually force you to process them, so that you have just a few for your game to use effectivelly.