I added a new plugin to the Movable Type Enterprise 4 instance called UploadDir (Japanese to English, Google Translate link). The “Insert Image” and “Upload File” dialogs normally only have two default options, “<site root>” and “<siteroot>/yyyy/mm/dd.” Then there is a text input field to manually specify another directory. This plugin auto-suggests an upload directory based on the three-letter file extension.
Blog administrators can override the default settings under Tools → Plugins → UploadDir. Below are the default options: