The ability to split and merge tilesets and framesets would be particularly handy, I think. So, for example, I could create several different tilesets for several different groups of objects, then create a conglomerate tileset that uses whichever groups of items I need for a particular map on a single layer (for solidity purposes).
Or (and this is probably less likely) the ability to lock two layers with two different tilesets but the same scroll rate together so that the solidity from both layers applies to either layer.
Also, when editing frames, I sometimes get "Error drawing transformed graphic" errors popping up twice in a row when I go into the frame editor view, but the matrix is perfectly fine. I think it has to do with the selected background frame from a previous view of the frame editor. And every time I tab away from the screen to type this message and tab back, another copy of the message shows up. I've got four messageboxes saying the same thing now. Five now.