Hooks and Filters like WordPress
Being able to modify core functionality without hacking the core is the most useful thing about WordPress. Drupal and many others have already jumped on board and began to incorporate these features. Joomla! needs to provide it's developers with a hook and filter system to allow app builders the ability to customize. Otherwise Joomla!'s just a brick.
Yes, I use dynamic overwriting of core files just to get things done in Joomla when there are no eventhandlers or webhooks. Problems arise when there are other plugins installed on a site doing the same thing. (example: the various extensions that try to hide modules by overwriting the modulehelper class). Huge problems with conflicts which are impossible to debug for site-developers. So events and webhooks are definately the way forward. Joomla is way behind on this one, so time to catch up.
There isn't anything in Joomla that can't be overridden. As a developer, I guarantee it!
What do you want to override? That might be a good extension for me to write.