One issue that I have run in to using this plugin is that when a site is moved between networks custom post type rewrite rules are not regenerated correctly, resulting in 404's for front-end CPT page requests.
This is problematic for those of us using the move operation to launch sites from staging networks to production networks. Manually flushing permalinks after a move is tedious.
A workaround we currently have in place is calling
delete_option( 'rewrite_rules' ) in a callback for wpmu_move_site. This forces rewrite rules to be regenerated on the next page request for that site, when all CPT's are registered. The same approach is taken in core, where they call
delete_option( 'rewrite_rules' ) after updating the siteurl and home options for sites that have had paths updated via wp-admin/network/site-info.php.
While this works for us, I think it should be incorporated in to the plugin.