We have worked on over 100 joomla projects and almost 20 projects of Wordpress.
I am fully agree with Ryan, that its largely depend on developers that what type of issues you face with site either it is developed in Joomla or Wordpress.
I usually make my decision based on following points:
- If site is niche based like for specific Industry. Joomla is better, as it has plenty of extensions available for specific industries like auto, realestate, event management, etc.
2. If site is multi-ligual, I choose Joomla. As it can handle multiple languages from within one system with really powerful options. Wordpress, we have to make separate installations for each language.
3. Multi-Template Website: Joomla can easily have different templatings for different parts of website.
4. If site is for small business, which doesn't need above complexities, I prefer to use Wordpress. As it is simple specially for end user to handle.
As far as SEO is concerned, Before Joomla 1.7, Wordpress was on Top. But now Joomla has almost same options. But definitely, as Joomla sites are usually more complex, SEO handling can be more complex.
One more thing, I am not sure about Wordpress, but Joomla's Admin panel is also fully customizable. We can make our own internal template, hide complex stuff for advance users only. And you can brand inner panel with your own graphics etc.