After scouring the internet to see if there is any new clear information on ways to handle custom post types with wp_get_archives, I see that there still isn't a straight forward easy way for newer WP developers to do this.
I'm just wondering why after many years now of custom post types being in WP (CPTs are awesome and I use them daily) there still isn't built in support for them with the wp_get_archives function? Custom taxonomies are supported as of 3.0 for wp_list_categories so it would seem that custom post type should have the same level of functionality.
The only easy way I know of to get custom post types to work with wp_get_archives is to use the out of date Custom Post Type Archives plugin and hack the plugin to make it work for pagination with your archives.
The only other solution, but not as user friendly, is I believe to use getarchives_where and then do some permalink rewrites to make the pagination work. But I'm not sure there is one place that explains both of these concepts together for newer users.
I see there is a ticket for this overall issue at http://core.trac.wordpress.org/ticket/21596. Just wondering if maybe the priority on this item should be moved up so as to enhance easy of use for Custom Post Types that much more.