There's a bunch of discussion around what we can do to make rendering and the theme system better.
Currently there are ideas blocked simply because sometimes theme() is called inside drupal_render() and sometimes it isn't.
Examples of things I've personally heard of:
- #1843798: [meta] Refactor Render API
- Allowing drupal_render() to handle processing/altering variables before theme() is called, so theme() itself could become optional for certain types of render arrays
- Allowing drupal_render() to handle ensuring "drillability" for renderables with more advanced inline "default" rendering behaviour - http://drupal.org/node/1986116#comment-7459028
I'm sure there are others. We should just cleanup what direct theme() calls are left in core so it doesn't hold back refactors elsewhere.