It certainly would be nice if any/all classes could be extended, but some things it's just not practical to be able to extend on the fly. Personally, I still have to hack on 5 files (not a major task) on an upgrade.
These are the ones that I still have to edit the PHP files on...
library/XenForo/Model/Avatar.php
library/XenForo/ViewPublic/Helper/User.php
library/XenForo/ControllerPublic/Abstract.php
library/XenForo/Helper/String.php
library/XenForo/CodeEvent.php