Suggestion: Change the theme to allow the use of logo and favicon images that reside OUTSIDE the theme directory.
If we could do this, upgrading would be SO much more simple. Nothing would need to be added to what's in the zip file at all, unless the user had customized some of the code. As is, I have to copy custom images into the theme directory every time I upgrade. I don't use the rotating header images, so I don't know if this suggestion could also apply for them.