I would like to suggest the ability to change the profiles.conf using a separate utility that will either directly edit the profiles.conf or create a new file with the edits to use. Suggested edits include bit rates for audio and any other tweaks that would be easy to implement that users may want to change. I notice that 160kbs isn’t cutting it for my ears, so others may feel the same but might be afraid to edit the file directly. I did try to keep original audio and time it up with converted video, but could not get it to work. Unfortunately, most of us just don’t have a good understanding of the command line arguments and generally tweak code found on the Internet instead. It would be nice to try and bridge this divide and create something more user friendly.
Also, it would be great to be able to keep edits of profile.conf with upgrade of MCEBuddy unless it would cause a conflict with upgraded ffmpeg and handbrake versions.
Regarding the profiles.conf, you can create a custom profiles.conf in a separate directory outside of MCEBuddy and point MCEBuddy to it from Settings → System Settings → Custom profiles. That way even after an upgrade it will always use your custom profiles.conf file and not overwrite it. MCEBuddy.conf is always preserved through upgrades, not profiles.conf because of changes to default profiles and their interaction with underlying encoders.
This would be pretty cool and probably very hard to maintain due to all available combination of parameters that ffmpeg and handbrake offer. But if you exclude that ability the framework of what is within a profile entry is set by MCEBuddy so basics could be available to manipulate via a UI.