In reply to Simon.

You may want to check out the Roots theme, if for nothing else for its theme wrapper and its modular organization of template files.

The WordPress theming system is very flexible and themes don't have to be the way that you describe.

Although the default themes (which I'm pretty sure you were looking at) probably aren't the best example if you're looking to develop from a DRY (don't repeat yourself) approach.

P.S. This was supposed to be a reply to Simon's comment. Must've messed up the reply link click.