Currently the stylesheets ie.css and ie6.css are included directly in page.tpl.php.

This is bad for 2 reasons:

1. They do not get included when aggregating/optimising CSS.
2. With this mechanism, themes that use this one as a base don't correctly load these.

There seem to be various solutions to this, but have not looked further into this:

Use a module - http://drupal.org/project/conditional_styles
Use template code - http://drupal.org/node/744328