Hi,
I'm currently busy writing a new theme for Drupal 7.
It's not the first one I do, my first try was with Saeven for Aegir 2 years ago but it was mainly for my personnal/work purpose.
This message is to get a feedback from the community on how to implement best practices for creating a base theme.
In this project, I tried to decouple it as much as I could and what, actually, makes a theme.
The current issue with Drupal is that, currently, many theme definitions are defined either in theme_function() or via templates.
It's a huge inconsistent mix, especially when theme_functions() are used.
It would be actually very easy to replace those with a template and its set of pre/process functions.
And that's exactly what this theme does.
Almost all the D7 core theme definitions has been altered to use a template and thus pre/process functions properly.
Also, I focused on providing only render arrays in those functions, so, the render() function in only used in templates files.
I invite you to read the readme which describe a bit more how the theme is working.
The theme is bundled with two subthemes that you can try and see how they are done.
I'm looking forward to get feedback on this!
Thanks!