The current upload process for file upload assignment submission is pretty clunky for students, as they have to choose each file individually by browsing to it in their file system.
Students expect to be able to just drag multiple files in. This is supported for uploads to the Files area, so I don't see why it shouldn't be for submissions as well.
A related idea is allowing selection of multiple files when choosing from the file system: Allow for students to select multiple files by using SHIFT key to upload without selecting them one at a time!!