It would really pain me if the default Jekyll site were XHTML. That'd be bad for the internet.
Instead, use Twitter Bootstrap as a base (while still keeping @mojombo's origin design), to give users a great initial baseline to build beautiful, simple sites.
Defaults are more than just the starting point. It's what 80% of users are going to use. Look at WordPress and the default theme. May as well lead by example and start the user off right.
* Add Bootstrap base CSS as a better reset and base layer
* Update default layout to HTML5 with boilerplate best practices
* Add title and post date to post.html (rather than including in the post itself)
* Make site title a variable and add to _config.yml
* Add page title to header
* Add default .gitignore to ignore `_site`
* Remove unused `rss.png` and `.gitkeep`
* Add Modernizr for legacy IE support