After spending some time editing, I thought of a new feature that would be helpful. It would be cool to have some sort of palette with different presets you could apply to the currently selected sprite. You could set all of the values for the setting (depth, scale, layer, and pattern), and then give that setting an appropriate name, like Text, Background, Pick-up, or Enemy. Then whenever you come across a sprite that should have those settings, you just press the right button and they get applied.
This would help when editing animations. Each time the animation changes to a new frame, sometimes all of the settings will change as well. Then you have to go through and adjust each setting by hand again, hit the Adjust button, and then do it again for the next frame.
It would also help when editing large sprites that are made up of separate groups or game with complex backgrounds that you want to have a consistent feel.
Finally, an undo button would be nice. It drives me crazy when I accidentally hit Delete. That might just be me though.