Yeah, but if a client wants something custom you're stuck either modifying an existing plugin, or creating a new one, and creating Wordpress plugins is a godawful mess.
No one is arguing that WordPress is better, necessarily, than a custom build. But reality trumps theory. Theoretically a perfect diet may be out there, but if you can't afford it and won't adhere to it, for example, a less-theoretically-perfect diet that you can afford and can actually follow is better.
A lot of times I or my client can't afford a developer for a custom app. WordPress solves that problem, and I think it's only getting better, simpler, and more stable with time (as all open-source projects kinda do).
It's pretty straightforward and easy imo.
Trying to integrate several different WordPres plugins is a challenge, as they each tend to be written in their own style.
Having said that, there are guidelines and best practices found in the codex (for one, all the hooks and filters that are available which are generally well documented) and there is some quality control when submitting plugins to the WP directory. In addition to that there is a fantastic handbook (professional WordPress plugin development) that gives both beginners as well as veterans a healthy education in the best ways to write plugins. And there's a big blogging community writing detailed tutorials.
I'm not sure what you mean with integrating plugins - what does that accomplish? Most plugins run fine when running concurrently on an install.
A lot of these criticisms toward WordPress in this thread are a bit ridiculous if you ask me. Yes it's written in PHP, big deal. Yes there's a lot of code that if written afresh today would look different. Yes there's variable quality in code written by various plugin/theme developers. At the end of the day WordPress is plain accessible for people - and that is a big reason for its success.
I started out years ago knowing zero about code to where I am today. My first plugin was shit and know I'm getting pretty good at it. Because developing on WordPress has been so much fun I taught myself Php, html, css, javascript (including ajax and jquery). Clearly, I'm not the only one as it is the most active community of all the CMS choices out there - and a lot of people are making a living thanks to it.
By integration, I mean adopting plugins from various authors and making them work as part of your theme. There are all sorts of issues involved... random visual design, clashing HTML doctypes, possible poor coding, adding functionality, fixing security issues... creating a coherent, secure and functional site by piecing together various WordPress plugins is not as easy as installing some plugins and whistling off into the glorious sunset. Simply finding a plugin for a certain purposes which actually works can be a challenge.
I wasn't attempting criticize WordPress or PHP in general, just the quality of the average plugin and the lack of consistency and order.