This is a huge discussion, but I think Dion covers most of the important aspects in the Trac ticket.
Things that are important in my opinion:
A few more action hooks, that maybe could become sort of standard if introduced by the default theme, helping plugins work their way easier into the content/functionality of a typical WP site. E.g.:
... before and after
the_content(), so that plugins can add content without resorting to filtering.
An Options page, to tweak very basic things. This page would also help theme authors in general, as a model; now it is not easy building options pages for WordPress.
HTML5 doctype. Enough said!
Sensible typography! Seriously! No things like
text-align:justify without hyphenation, or
An application named WordPress should have better typography than that. And good web typography is rather easy to achieve these days, with so many knowledgeable people working on the subject and sharing the result of their work. (See number of CSS frameworks.)
See, as an example, the typography on op111.net: http://op111.net/
It is a theme I’m putting together, very plain and simple on the surface. Its typography is almost default Blueprint CSS -- http://www.blueprintcss.org/ -- (I’m resisting the temptation to mess too much with Blueprint) and I’m surprised by how good it looks by virtue of the sensible typography alone.