In the Hydrogenaudio discussion thread's metrics table, the new encoder scores better than Core Audio. But this is at constant bitrate (CBR) [edit: maybe not? see lesscraft's reply below]. Core Audio also has variable bitrate modes (TVBR) which the new encoder lacks.

So maybe Core Audio will continue to be the best when TVBR is available, but I'm hopeful the new FFmpeg encoder will be "good enough", especially if more folks find and contribute problem samples to help tune it.