I see that WordPress 3.0 has a lot of potential, however, I'm quickly discovering some of it's short comings. And this is on a fresh install of WordPress 3.0 and not an upgrade.
1) Taxonomy and term support in PermaLinks - There is really no support for this unless you create a custom post type. What I mean is that I want my permalinks to read site.com/taxonomy/term/post-title or eventually, site.com/taxonomy/term1/term2/post-title. I can create my taxonomy page with no problem thanks to creating a template and then applying that template to a page. Whenever I create a page though that is assigned to the custom taxonomy, it doesn't pick up the taxonomy. So I've created custom post types that will look at the proper slug in the rewrite section.
2) Custom post types and page attributes - I can see the parent drop down in here, but I can't see the template drop down, no matter what theme I am using.