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, 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 $file->cached set). Steps and configurations are also alterable on load and save.
Media Mover previously supplied hooks for stopping a file from processing if particular conditions were met. This is function has been updated to hook_media_mover_process_control which is called before media_mover_file_process_pre and media_mover_file_process_post. For example, if you do not want a processor intensive task to run when the server load is above a certain amount the mm_utilities module can stop processes from running. The pre and post hooks allow modules to catch completed file process operations and perform tasks like notifications, updates to nodes, or other options.
Media Mover is now dependent on the Drupal Queue which allows for better control of how items are processed. It is still possible to process a single file without ($configuration->run_file($file)) running through the queuing system if you need to convert files on demand, however all other file processing is done by the queue.