I propose the removal of all direct access checks placed at the start of all classes:

<?php defined('SYSPATH') OR die('No direct script access.');

This check makes classes unusable in other non-kohana projects without first having to define 'SYSPATH'. This line of code doesn't conform to the DRY principle since it's repeated a no end of times throughout the kohana core. This removal will make classes that little more cleaner and be another step towards removing all global state.

To still prevent people from accessing class files directly; index.php (or a symbolic link) could be placed in a public folder, or a htaccess file could be used.