One feature I miss from MAMEUI is the ability to organize your favorites into subfolders. You can create your own custom .ini file, load it, and then add favorites to it.
If possible, do this both for MAME favorites and for MESS software list favorites.
Also, the MESS software list favorites should be stored in their own file rather than burying them in qmc2.ini. This matters if I move to a new PC and want to easily copy over my favorites.