Some words of wisdom to Drupal newbies: It's still interesting that after following the Drupal biblical proverb "Don't hack the core", I see a lot of people still making suggestions to change things in the core.
I also see a lot of Drupal websites where Zen was still used and changed from there (or the Twenty Eleven theme on Wordpress). I think the right thing to do is create a subtheme or copy the zen theme to sites/all/themes and create your own version of it. This way, if Drupal or Zen gets updated, you won't lose your changes. If you feel that you MUST hack a core module (and there really is never a reason for doing this) because of a time constraint or client deadline, backup that directory first and be prepared to restore it. Actually, I believe that everything in Drupal should be backed up regardless.
This is an opportunity for web designers who embrace Drupal to get better at Drupal hook programming and to develop the habit of using the sites/all directory to put themes, modules, and whatever else. If you don't like, for example, what the pathauto module is doing, but see its value, there is nothing wrong with developing your own pathauto2 module, and designers need to keep in mind that if there are updates to any of these modules, their changes will be overwritten.
Just download the contributed module and upload it to a new directory in sites/all/module, change your .info files, and then hack away at your new module. This way, if it fails for some reason, you always have the original core or contributed module to go back to. This is my solid approach to learning how to program modules and the hook system. You can go hog wild with your own module and if you mess up, you disable your module and re-upload the original.
Drupal, Wordpress or any CMS are not just a way to do web design quickly, but some organization in the way you work with your CMS needs to be planned. Content Management Systems are always a balancing act.
I look forward to your discussion on this.