The more I think about it, what I really have a hard time with in EE is how templates have content. In all the CMS’s I’ve worked with, content has a template(s). That’s where my “backwards” opinion comes from. You can’t open up a weblog post and choose for it to be formatted using template alpha or beta, for example. I realize that a template displays content in both scenarios, but in EE, you alter your templates to determine which content is displayed, whereas in other CMS’s, you go to your content and choose how it will be viewed.
The open-source CMS that I think has the best implementation of this content/template model is MODx. It’s still in beta, so it’s missing some features that limit its potential user-base and preclude it from “mission-critical” use. It’s not necessarily the best-suited for a blogging site, either, but MODx just flat out makes sense to me (in a way that Drupal, Joomla, or Wordpress never did). My dev shop is using it on some pretty big sites and it’s holding up nicely.
Other than that, the CMS’s that we’ve developed in my company have never used a “templates have content” approach. In fact, all the developers in my group that are looking at EE are perplexed by this architecture. Just in my immediate group, our developers have written 3 CMS’s for different projects, and not one of them uses EE’s “templates have content” type of approach. That doesn’t mean it’s wrong… I’m not arguing with the fact that EE is incredibly flexible, full-featured, well-documented, and robust. But its approach is different enough for some of us to raise an eyebrow and scratch our heads. It’s probably just how we think about things.