@Jan Dembowski - "modifying the core files also means you are swimming in the deep end of the pool alone and by yourself" is not necessarily true. If you are prepared to study the code and know a bit about development and security it's easy to have the best of both worlds. Running your own svn and keeping track of changes, adding the code you want (particularly any security hardening the team includes) is a bit of work but its arguably less work than rolling your own blogging platform/CMS from scratch.

I sure wouldn't recommend this for everyone but its a perfectly valid reason for not updating carte blanche with WP's auto update and a great use of open source software.