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In fact this is how we've designed our base theme from the start. We've got a clean separation between the css that's required for functionality and the css and images that contain look-and-feel things like borders, colors, backgrounds, icons, fonts, etc. If you look in the base theme folder, I'll link to GitHub:

https://github.com/jquery/jquery-ui/tree/master/themes/base

but you can also find the same in the development-bundle folder of each jQuery UI download. There are 2 sets of files

Functional CSS:
jquery.ui.core.css - functional css that's central to the css framework, no look-and-feel, and no specific widget css
jquery.ui.PLUGINNAME.css - one for each plugin or widget that requires css, no look-and-feel, only specific widget css

Look-and-feel CSS:
jquery.ui.theme.css - all the rules that set borders, colors, backgrounds, icons, fonts, etc. for all widgets in the theme

So to get a skeleton theme css file, all you need is to include all the css files EXCEPT for jquery.ui.theme.css. If you're using ThemeRoller (which creates a concatenated file) it is included, because that's how ThemeRoller functions, it only modifies the contents of jquery.ui.theme.css. In that case, you can just remove those lines. Compare to the top and bottom of https://github.com/jquery/jquery-ui/blob/master/themes/base/jquery.ui.theme.css to see where that section starts and ends.

As for documentation on general CSS classes, see

http://jqueryui.com/docs/Theming

and

http://jqueryui.com/docs/Theming/API

and

http://jqueryui.com/docs/Theming/CustomThemes