I believe what you want here is a python script that will take in flat xml files, upload them as MWS Feeds, poll the processing status, and then report on the final status. I can write this in either Python or Java for you.
I can also write this in such a way that you can leave the application polling a directory and just drop new files into the directory when you're ready for them to be processed. Or, I can just set the application up to be manually executed for each file. It's up to you.