I think it would be great to give wordpress the capability to use sub folders in the theme for page templates.I.E. yourtheme -> pagesfolder -> productsfolder -> myproducts.php. This would just make the theme's folder allot cleaner.
Also, as I'm using wordpress more and more as a CMS. It would be great to see something like the tabs for the different menus in the menu section for the pages area. I've been using pages for everything from "pages" to just a snippet of content that's embedded on pages. It would be great to be able to organize my pages into categories or sub sections to keep everything neat and easily accessible.