To me it seems obvious what needs to be done to fix the somewhat difficult to use mess that is widget organization admin:
1. In the new interface, how about allowing the (sometimes very long) list of available widgets on the left side to scroll, so one could easily place it in the appropriate widget sidebar area? Currently (as before), one has to drag from way down at the bottom and HOPE the whole window will scroll up to accommodate moving the new widget to its area, which is a pain and sometimes does not work.
2. How about allowing the user to specify the number of columns in layout for both widget sidebars and available widgets?