In most cases an off the shelf content management system like wordpress or Joomla will be adequate, but there are custom projects that need a hand coded solution. You know your business better than anyone, and if it is determined that your business goals cannot be met without a bunch of workarounds using your cookie cutter cms then it's time for something better.
A great cms shouldn't require a manual, it should just be logical and simple to follow. This is exactly why we use a custom in house developed cms for nearly 50% of all the projects we do. Our cms couples ease of use with custom or semi-custom coding to meet your business goals. Some common content management features include: