I have a few ideas for your very nice plugin (and very well coded I might add).
1. on the theme header options page (/wp-admin/themes.php?page=custom-header) it would be great to be able to choose the headers for the custom post type archives. I know you can do this already for the CPT taxonomies, but not the main archive pages.
2. the ability to add a simple slideshow. this is probably out of the scope of the current plugin, but a simple fading one might be a nice touch.
3. ability to have more than one header size.
4. have the selected header only showing in the page/post editor. and an ajax link that expands to show all the options to choose from. That way if a site has 100s of headers it will still work fine.
I've already got my own codebase on the go that implements a few of these things, but your UI is better implemented. perhaps we could collaborate.