I've written many custom applications in PHP/MySQL over the years - from tiny to huge. Not having taken the time to learn the details of WordPress, I find it very frustrating to work with (under the hood).
Subjectively:
- Very poor naming conventions
- Execution flow is bizarre
- General lack of organization
- Hard to audit what happens when
- etc...
Their concepts of usability is great, and support for plugins is also great. I'd just love to see the system re-engineered with those principles, but with a disciplined and clear development methodology.
I'm sure the next guy would say "no it isn't, bla bla bla", but that is just my opinion after bumping into it (hosting, modifying) about 3 times.