This is interesting. I think that MIDI is indeed a very important thing in the harmonizer. My guess is that the problem is more in the control signal domain than with MIDI itself. Eventide will have to improve this greatly in order to give a good feel to the supposed "E-Control". If they manage to do it for E-Control, that will almost surely work for MIDI as well.
The harmonizer is a great machine for live performance sound processing. It would be wonderful with a better control domain / MIDI response.