I have a client who needs the original filenames provided by plup uploader. There's a couple ways to do this, but I'm not certain the best approach.

Best Fix: Add a multiplepart data piece to the request data containing the original file name, and an option in the admin to use that, or not.
Pro: Granular control
Cons: Fringe case, not sure enough people care to make this worth it.

Easy fix: Modify the plup.js file to handle unique_names set to off.
Pro: Quick fix
Cons: Obscure, fringe case support, and perhaps other conflicts I've not found yet?

As far as easy fix goes, I can provide how I've handled it:

In a custom module, I use element_info_alter to change set unique_names off.

/**
 * Implementation of hook_element_alter
 */
function custom_element_info_alter(&$cache){
  // Keep the original files names from plup uploads
  $cache['plupload_file']['#plup']['unique_names'] = FALSE;
}

Then, a patch would be required on the plup.js file. It currently builds the image style paths based on the file.name parameter passed during FileUploaded events. I was able to get my proper thumbnails by instead reading fileSaved.filename. - This modification is working with, and without unique names off.