Well, it may be nice! But the Command Line Interface (CLI) currently fits all my needs. If there is someone with good skills in implementing a GUI (either using Swing, AWT or SWT) and willing to contribute to this project, he can contact me to discuss this issue.
AC3 is not compliant to the MP4 container. The multichannel AC3 must be transcoded to a multichannel AAC. If anybody figures out how to do this on the command line, I will integrate it!