EE is much more flexible that WP or Joomla. You have so many more options about where content goes and how it's configured, yet it's easier to use, too (at least in my opinion). EE also doesn't create any code itself, meaning that you are in total control of the code output, which for me is a huge advantage. EE also has a huge number of quality add-ons and a very active and supportive community.
When clients question the cost over free options, I remind them that the time I save in setting up EE can easily outweigh the savings in using free code.