As Media Mover 2 finally moves toward alpha, I've taken the risk of doing some significant refactoring- or at least improvements- to make the transition to Drupal 7 easier as well as to provide a much more robust platform people to start leveraging.
Similar to Drupal 7's [hook_file_load](http://api.drupal.org/api/function/hook_file_load/7), Media Mover now offers hook_media_mover_file_load() and hook_media_mover_file_save(). This allows for easy altering of files as they pass through the system. These are both cache aware so you can still benefit from caching while having the ability to avoid modifying a cached file if your modifications are not dynamic (cached Media Mover files have $file->cached set). Steps and configurations are also alterable on load and save.