I've been wondering if there is a way to manipulate effects that are applied to layers. I don't currently see any method to do this.
Perhaps a change in the way Layers are handled by the event editor is in order. Currently there are Layers actions in the System object, and you can do a System Compare on Layers info in a condition, but there isn't any way to access the effects applied to a specific layer to change them.
The idea I have is to separate Layers from the System object, the event editor would treat each layer as it's own object. This way you could more easily create conditions and actions directly with specific layers if need be, and you'd have access to each layer's effects the same way you do for objects like sprites.
I don't know how easy it would be to implement, or if this is too fundamental a change to Construct, but it's just a thought.