Elements that still can't be themed:
1. Column Resize Widgets in Open/Save dialogs.
2. Blue/Graphite hilite around text boxes.
3. The resize square in Finder windows (where the horizontal and vertical scroll bars meet).
4. Shadow thicknesses? (I don't know if you can do this with Shape Shifter or not, but it would be cool for a flatter-type theme to have flatter-type shadows)
5. Throbbing default buttons (you know what I mean). You can't stop that animation or even change it without chaning the "pressed" state of the button.
6. The gradient in brushed metal windows? (can you remove the weird gradient from the brushed?)
7. Metal textures.