I think it would make using Paint.NET, if it simplified the number of windows needed for major functions.
Some examples of innovative design:
I recently released Babya PhotoPro , which has a innovative design: by making use of fewer tool windows, with the most important tools are kept in the main window with auto hiding panel areas -see the screenshot:
http://www.softpedia.com/screenshots//B ... oPro_1.png
That hiding panels concept works well-it's de-cluttered and I love working with it.
Even if the various palettes could be docked to just a icon as in Adobe software, or a Office 2007 style ribbon interface it would be much cleaner.
Study these programs UI design-and I think they are the role models.
Just some thoughts about UI design-you don't have to change anything-this could wait until v 5.0.