The problem with this solution is that many critical files can't be symlinked. It is especially with configuration files, usual way to handle it - create a new version and replace the old one.

Symlinking of directories can help but again it can be a problem with some software and nobody knows which one exactly.

Additional (but not critical) issue - read speed of small files (usually - shell scripts in /etc or localization files in /usr/share/locale or Hildon icons or X11 fonts) initially would be degradated until it sits in kernel cache. Because that files are used pretty often in "search" mode (file-by-file) it would visibly increase an overall access time.