I think that if MT offered a feature similar to the Widget Manager (drag and drop of "modules") to build the whole blog AS WELL AS a nested tree view of the blog, it would allow almost instant customization and building.

For example, if users where able to view and drag and drop the following modules into the interface, it would facilitate the construction of a template. The tree view would also easily identify where the output is generated from.

CODE
MAIN INDEX
  -> HEADER
  -> ENTRY SUMMARY
       -> entry-title
       -> entry-metadata
       -> entry-body
       -> entry-footer
           -> Categories
           -> Tags
  -> FOOTER


If you wanted to go to the extreme, you could combine this with a "snapshot" view of the template with the container, content, alpha, beta, etc. This way, if someone wanted, they could just drag the gamma column out of the layout and it would disappear altogether...