What about "One File per Class" for Admin and Public Controller?...
I was thinking about this and find only one way...

MY_Controller.php_' is for '_Site_Controller class

Admin_Controller.php_' is for '_Admin_Controller class

Public_Controller.php_' is for '_Public_Controller class


and at the end of MY_Controller.php include other Controller classes:

class Site_Controller extends Controller
{
[...Site_Controller class code...]
}

include('Admin_Controller.php');
include('Public_Controller.php');

/*  End of file MY_Controller.php */
/*  Location: ./system/application/libraries/MY_Controller.php */

...but the best way will be to include Admin_Controller when we are using backend of the site... and Public_Controller - frontend... I think for doing this we need to do some CodeIgniter Core Classes code changes...