The usual wordpress install runs an entire site, which results in putting all the wordpress core files in the root of the website. Core files and site specific files are mixed together. Currently only the wp-config.php can be moved outside of the document root, but it usually isn't. The typical setup looks like this:
/webroot /.htaccess /index.php ... core files ... /wp-admin /wp-config.php /wp-content /plugins /themes /uploads /wp-includes
I'd like to see the wordpress core files moved into their own directory. Not only is it less cluttered, but it becomes clearer to the less-advanced user where their files go. Also, When checking into our own version control repo, it's easier to use svn:externals (or equivalent) with the wordpress.org repo.
/webroot /.htaccess /index.php /wp-content /plugins /themes /uploads /wp-config.php /wp-core ... core files ... /wp-admin /wp-includes