CI was built in the PHP4 days, and for that reason it has a lot of cruft left over. For example, there is no autoloader. Also, classes are loaded as singletons, and are assigned to properties of the controller, which I put into the 'magic' category, and isn't compatible with IDE autocomplete features (I'm a VIM user, but it makes things easier for a lot of developers).
//CI Class Load Example:
$this->load->library('example');
$this->example->something();
//Raw PHP Class Load Example:
$this->example = new Example();
$this->example->something();
As you can see, the latter is a little more obvious about what is going on.