Aside from the fact that, well, everybody else has already thought of doing that, it turns out that it isn't such a great idea anyway.  Here's why:

• It's clumsy for your users to put commands into little text files, unless you give them a program that makes the text files for them.  But if you do that, you might as well give them a PC program (created for you in seconds by HIDmaker FS) that sends the data to your device directly, without all that FAT file system complexity and expense.
• You make a monstrosity that confuses the user.  When a user interacts with a device that represents itself as a disk drive (like all Mass Storage Devices do), he instinctively has an expectation that your device is going to store the file.  But your device isn't going to store the command file, it is going to consume it.  So your customer calls your Tech Support number (which costs you money) to ask "What happened to my file?"