One thing I ask is that you make a human-readable file system, for the love of God. Please don't go the way Ryu is going, make a folder system that is easy to back up and sync across multiple machines. Not everything needs to be a bunch of random numbers and letters. Create a simple user folder structure based on the username. Under that, create a save folder structure that includes the game name and title ID, something like /USERNAME/GAME-ID/SAVES/.
I know this isn't a high priority, but it would help people who use your emulator to sync and save their data easily with tools like Syncthing. Additionally, for that reason, keep the app settings outside of the user folder, and don't forget to include a portable mode.