In reply to Jeffro.

Given the way things sometimes can get... taken out of context with the Theme Review Guidelines, I just wanted to clarify. It's been mentioned on the mail-list as a good example of a best-practice implementation, but that's it. If it gets widespread adoption, adding it to the Guidelines is a bridge that may present itself for crossing, sometime in the future. :)

As for Theme portability: that is a very important consideration in the Guidelines. To the greatest extent possible, users should be able to switch from one Directory-hosted Theme to another with minimal impact - and with zero impact to user-generated content. So yes: the Theme Review Guidelines do prohibit Themes from including post-content shortcodes, and from registering custom post types, custom taxonomies, etc.

The presentation-vs-functionality differentiation has been hotly contested at times, but I think we're finally seeing inroads with both end users and developers understanding why it is best for everyone involved for Themes to keep as closely as possible to presentation, and to leave functionality to Plugins.