Hello there
I am not too happy with how files and folders are arranged, and as one consequence I find the process of upgrading WP rather "difficult" : while some directories can be scratched with newer files with no hesitation for most users (wp-includes, wp-admin), the root directory is more questionnable.
In the root dir, there is a mix of files that the average user won't ever tweak (wp-feed, atom, trackback etc..) and files that everybody modify (index, wp-comments and .css)
I thought it would be easier for most users to have folders of files you can safely overwrite, and have a root dir with only the "personnal"files.