Here's a list of things I noticed that might you want to improve. Some maybe a little too specific, but that's up to you to decide.
-Exclude images/slots from exporting to atlas
I setup my projects to have the complete character in the background as a reference, but it is also exported to the atlas. This may be solved if the reference image can be set as a background image, but before exporting I now need to delete the reference image first.
-Fine grained control for positioning images
I would like to use arrow shortcut keys to position a slot image with little increments
-automatic slot selection for dragging does not always work, sometimes it's better to highlight the slot in the tree and drag
-additive blending does not seem to work
-clicking in an empty place in the dopesheet does not select the frame, you have to click in the bottom bar
-when there is no selection in the hierarchy, selecting a key in the dopesheet highlights it, but the UI won't show the values of that key properly
-I would like to be able to set bezier curves as preferred curve for every key
-I would like to see a value graph for animated values so I can see the result of the transition curve directly on the resulting values.
-More complect predefined key transitions (bounce etc.) For one of my animations I wanted an elastic bounce effect. I needed a number of keys to reach this.
-Masking of images (for instance an eye ball) In my current animations I could get away with an eye ball behind a body cutout, but I can imagine cases where there would be no room to move an image behind another one. In that case a fixed mask on the animated image would come in handy.
Roland