In his latest post to his blog Lukas Smith looks at what things users and developers seem to hate about most of the content management systems available today (not just PHP-specific either).
This is just a quick start for a brainstorming of what we all hate in todays CMS (I am including portal/community software here as well and I guess most also applies to web shops) software out there. I have written a very small CMS application myself ages ago so I do not have experience in what its really like writing and maintaining a big one. All I know is that its insanely painful to deal with any of them, though if your site is all about having admins managing tons of static content or end users wanting to interact, there is little way around these ugly beasts.
Other "hated things" he mentions include the way that admin settings set stored in databases, the choices most of the software have made on their model layer and the lack of a quality API to extend the base functionality of the application.