The LevelWindow handling is quite complex (and messed up) and old. A lot of effort is taken to search for the image that should be displayed in the level window widget. I think this could be strongly simplified by just using the selection mechanism of the data manager view and beeing able to manually select any image with the context menu.
This could lead to a substantial speedup, as one user on the mailing list is reporting that the LevelWindow code is time consuming: http://thread.gmane.org/gmane.comp.lib.mitk.user/813/focus=822
(I don't know if this is 3M relevant)