Trankusa.. su or whatever
Layers are much more effecient than simply using graphics. You could imagine layers being used for Platform based levels wich have a background imagine in them. Doing this with seprate files and the editor in its current state would require you to script your own system for it (not everyone can do this).
Aside from the fact that its usefull for platform based kind of levels there is also the aspect of being able to over lay tiles. You can already do this with graphics but this would require you to use alot of image files or make alot of little setimgpart's. If you would merge it all into one simple layered tile editor it can save you alot of trouble, for it is easy to work with and it looks more organized.
The aspect of being able to layer tiles will automaticly give room for more creativaty and don't give me thats not graal style bull cause than you'd be better of playing some illigal 1.3 server with the original cool and leet classic style like you love it. (Sorry for that but seriously.. I mean it >.>)
back to layering tiles. E.g you want to create a nice floor and have some grass go over it.. you simply put the grass tiles on the layer above the current one and make them go over your floor. You could do this with seperate images or one big image but in the end its just more sexy to do it layer wise
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PS:
If layers are implemented it would be best to have a series of 6 layers
-6 Top (sky?)
-5 Above player
-4 Items, Objects/ Player
-3 Above first floor
-2 Underground (First floor)
-1 Bottom
Being able to use 32 bit png images with it and than you would be able to create some fine levels. (ill explain later on.. got crazy ideas but I noodles)