Is there any way to have a Custom Post Type panel with Post Type Archive page links in the Appareance > Menus Nav Menus section? Just as if you were selecting pages, including CSS classes for selected items.
Also, are you planning to release a WP feel theme-ing of your plugin? If you're not kind with this, will you accept patches to?
Now that WP Post Type UI is no more under development this will be highly appreciated and not so hard to do. Loved that UI. :)