I'm learning WordPress (I'm a Movable Type convert) and I think the way the installation files are organized is pretty lame for a dynamic publishing model.
In your WP installation folder, there are 23 files and 3 folders (/wp-admin, /wp-content, /wp-includes).
It would be super clean if it looked like this:
<strong>wordpress</strong> index.php /wp-stuff (or something like that) /classic /default /mytheme
When you're customizing WordPress, only your theme folder is relevant (or at least should be if you want to be upgrade-proof). But you have to drill through 3 folders just to get to your relevant files. Everything else is just junk in the way. The file structure should communicate the usefulness and relevance of each file/folder to the user. As it is now, the hierarchy is meaningless (except to those who wrote WP).
Clean it up and simplify. Then WP will be even more awesome.