There are a few key FFmpeg compatible audio codecs that are currently missing in Pro.
libvorbis - the official vorbis encoder that's better than the experimental one currently in Pro and was in Classic.
libfdkaac - Probably the most important one imo. I know you can't just include this one in the program by default cause of licensing but maybe you could do what you did in Classic where you download the file separately and put it in a folder somewhere?
libtwolame - I'll admit this one's really not that important (and wasn't even in Classic anyways) but I think i'd be nice to have, since it's (in my admittedly limited experience) much better than the stock MP2 encoder in FFmpeg.
Thanks in advance!