How to move theme directory but not plugins/uploads out of WordPress root directory?

http://codex.wordpress.org/Function_Reference/register_theme_directory

/**
 * Register a directory that contains themes.
 *
 * @since 2.9.0
 *
 * @param string $directory Either the full filesystem path to a theme folder or a folder within WP_CONTENT_DIR
 * @return bool
 */
function register_theme_directory( $directory )

You should be able to call register_theme_directory('/full/path/to/directory') and thus add a new path full of themes. This eliminates the need to use any defines as you’re attempting to do. You could do this in a mu-plugin on each installation, to force the whole install to have those themes available.

I would leave the default themes in the wp-content/themes directory on each install, and just add your custom themes in your new theme path.