There's only one thing missing, that would be nice: Encoding validation.
I recently had ripped some CDs and found there was a FLAC error which wasn't caught by MC (the Secure rip, no errors confirmation was the only status reported). While the rip was secure, and the bits were read accurately, the FLAC file had a bit error that caused an audible click. Testing the FLAC file with flac.exe verified that indeed the FLAC was corrupt.
I ran flac.exe in test mode on all my FLACs and found one more that had an error; it too was produced by MC.
It would be nice, for the file formats that allow such, to enable a validation phase to be run on the encoded file.