There NEEDS to be a much better way to store all user settings for the interface. Right now there are some settings that CAN be saved and restored, but others cannot. I recently had 3DS max crap out on me and drop all of my settings. Luckily, I saved out my Custom UI scheme the day before, but many things do not get saved, so I need to manually fix them. I feel that at least the following items should be completely saveable and restorable, and preferably transferrable reliably and easily from installation to installation. Particularly useful when setting up a new machine, etc.
1. User installed Scripts
2. Keyboard Shortcuts
3. Menus
4. Material editor layout, default materials, etc.
5. Toolbars
6. User Paths
7. System Paths
8. Modifier Sets
9. Quads
10. Colors
11. Mouse
12. ??
Please feel free to add to this list. 🙂