The purpose of this theme is that it can be used to start a new theme from, eeehh, well… scratch.
So the theme itself is as empty as can be. That way there is no need to remove everything every time a new theme has to be developed.
Version 3.x – only available for Drupal 7 – is a HTML5-version of this theme.
Most core CSS is left in place, in template.php and scratch.info an example is given how to remove or overwrite those CSS files. If you want to remove all CSS from core or loaded modules take a look at the Unset CSS module or the Mothership theme.
When making this theme HTML5, I borrowed a lot from Boron. And new features I would like to add might have a lot of resemblance with the aforementioned Mothership theme, which approach I like.