Issue: Client wanted to migrate their WordPress.com site and retain full functionality in a WordPress.org site.
Long/Short: This is not possible to do, as the WordPress.com sites have built-in features exclusive to only WordPress’ own hosting platform. Note in the article that you can only use Tools/Export to an XML file (or, of course, pay $129 and they will export everything for you). When you do this, it only exports posts, pages, comments, categories, and tags. It DOES NOT migrate your existing media uploads and images; these, you will have to migrate manually.
Read more (from WordPress.com): http://en.support.wordpress.com/export/
Resolution: Export the XML file and import into your WordPress.org site as mentioned. If you have access to the MySQL backend, export the MySQL database to a .sql file, edit it and rename all the links to the new domain. Download each file from the media library and import it into the new instance. Remember to change the links to point to the right media file.
Problems: Remember previous features may not be available, even if you use the same theme. The themes they provide are customized and made easier for users. If you need further help (design related), then you will need to find an experienced developer who can edit themes and customize it to your liking.