I had the same issue with the latest HTML conformance checker of the validator on this new theme I’m developing. I found this solution:
remove_action( 'wp_head', 'feed_links_extra', 3 ); // Display the links to the extra feeds such as category feeds
remove_action( 'wp_head', 'feed_links', 2 ); // Display the links to the general feeds: Post and Comment Feed
remove_action( 'wp_head', 'rsd_link' ); // Display the link to the Really Simple Discovery service endpoint, EditURI link
remove_action( 'wp_head', 'wlwmanifest_link' ); // Display the link to the Windows Live Writer manifest file.
remove_action( 'wp_head', 'index_rel_link' ); // index link
remove_action( 'wp_head', 'parent_post_rel_link', 10, 0 ); // prev link
remove_action( 'wp_head', 'start_post_rel_link', 10, 0 ); // start link
remove_action( 'wp_head', 'adjacent_posts_rel_link', 10, 0 ); // Display relational links for the posts adjacent to the current post.
remove_action( 'wp_head', 'wp_generator' ); // Display the XHTML generator that is generated on the wp_head hook, WP version
Not very effective for SEO and people with disabilities but at least helps the theme validate html5 in the validator for the time being, until html5 is final 
Cheers,
Onur
PS: I also googled for it myself for hours, and found the above solution in here: http://webdesign.anmari.com/2546/wordpress-html5-validation-bad-value-for-attribute-rel/