Right now FME Server and FME Cloud allow the user to upload (or select from the resources) any file they want as a source dataset e.g. if I set up a workspace with a Shape reader but the user uploads a DXF file it's just going to fail with some horrible error messages. That's not very user friendly.
What I'd like to see is an option to disallow uploading/selecting of unsupported file types, kind of what the Desktop version is doing at the moment. It can still be circumvented, but this would prevent a lot of the accidental cases.