On the other hand if your project is heavily dependent on CMS type functionality, Joomla begins to look better considering the features built-in to it's core. There also seem to be more advanced, feature rich themes available in the Joomla community. I wonder why that is?

I'm not knowledgeable of it but have you seen the GPL RokIntenseDebate plugin? It was created by RocketWerx (RocketTheme)
http://joomlacode.org/gf/project/rocketwerx/
"Two simple plugins that make adding IntenseDebate comments to your articles extremely simple. RokIntenseDebate consists of a content plugin, and an editor button plugin. All you do is write your article, then click the button to enable IntenseDebate comments at the end of your article. Only setup is to enter your IntenseDebate account number in the content plugin before using"