What I mean by this is others have a better structured, more solid & easily extendable code base, better separation between presentation and logic, etc.. Obviously, this is somewhat of an opinion, and it only refers to the underlying structure. For the end user, WordPress is probably the best. A large part of this is due to its ecosystem of plugins and themes. You shouldn't need to build custom code on top of WordPress unless you are doing something very unique, building an application (as opposed to a "website"), or attempting to tie together several plugins.

Sticking with PHP, both http://modx.com/ and http://www.silverstripe.org/ are fairly popular and well-built. I've also heard good things of http://www.concrete5.org/ , http://www.movabletype.com/ , http://textpattern.com/ , and http://ellislab.com/expressionengine . http://habariproject.org/en/ has also been built specifically to address many of the faults in WordPress and other popular systems.

Isn't MoveableType in Perl?

Possibly - I've never done anything with it. The PHP statement was really only for the first two, sorry for the confusion!

depending on what type of project you are building you might want to have a look at yeager (http://www.yeager.cm). although the site states beta, the tool is stable and used in live environments since several years.