This was in works for some time, but due to many changes in WordPress meta boxes, I was reluctant to complete it. Now, that things are finally sorted out, Pro version taxonomies/terms manipulation from post editor is much improved. Also, WordPress 2.9 is now minimal requirement.
All changes this time are for Pro edition, and nothing of this will be part of Lite. As you can see on the image on the right, button is changed to slick designed tag icon (Fugue icon pack), and drop down menu is added to the button with shortcut links. Menu shows all taxonomies for the post type (yes, it works with custom post types). Click on any of the options will add selected text as a term for the selected taxonomy. In WP 2.9 you will see only non hierarchical taxonomies in this list.
Click on the button, opens already implemented dialog with search/replace functionality. This time is improved to support custom post types and to turn terms into shortcodes, not direct URL’s. With that you will have no URL’s hard-coded for terms linking, and plugin will render shortcode as a link. More options there will come soon.
Many bugs (mostly WP 3.0 related) are fixed in both plugin core, widgets and tinyMCE editor integration.
As I said, all this is only for PRO version of the plugin. Lite version will remain to feature only managing of custom post types and custom taxonomies, all advanced features are for Pro only.