There will now be only two theme bases, developer and superuser.
This will essentially make the theme base concept only relevent to the developer that wants to strip away all the theme options and extra bloat. And so the average user won't need to be concerned with this. Hopefully this will provide a better on boarding experience for new users.
There will be a section in the theme options for selecting styles for the following, which can then be configured:
Header
Content (#276)
Footer
To keep the modularization of of the different style types, there will end up being redundent options between them (for example two header styles might have similar options) but they should be kept in separate files and saved completely separate from each other. For example header_agent_bg_color opposed to header_bg_color (including logo). This will make it easier for the user to swtich between styles in the customizer.
developerandsuperuser.header_agent_bg_coloropposed toheader_bg_color(including logo). This will make it easier for the user to swtich between styles in the customizer.