I don't think layers is a particularly necessary or useful feature for editing tile/sprite graphics, and would make the graphics editor unnecessarily complex for a game development kit. Cells are kind of supposed to represent layers themselves. If you need multiple layers, you can work with separate cells and create a composite tile from them in the tileset editor, (or just paste them together in a separate cell). That doesn't mean you can't use a graphics editor that supports layers to create a graphic sheet ot cell. I just think that it would be too much to integrate into a game creator... it's better left to the "import" feature, IMO.
