At the last Florida Drupal meeting one of the attendees (sorry, I'm horrible with names) asked why Drupal was so difficult to upgrade.  At first we were a bit confused since we thought Drupal was easy to upgrade but we later found out that the user was storing his modules in /modules and themes in /themes so every time he wiped out his Drupal installation he had to re-install all of the files for his modules/themes.  While it sounds like this is uncommon, I can assure you, it's quite common for new (and some experienced) users to make this mistake.