My abbreviated incomplete super-list:
USB on both for easier data transfer and vst software
Higher sample capacity for DIgiPro for higher-rez wavs
Option to toggle high precision knob tweaking vs midi precision
Fade in/out for MD samples
Modulation effects
Mute trigs/track
ASDR envelope page for MD tracks
Retrig function on MM acheiving 32nd or 64th note and smaller subdivisions
Reverse function on delay and/or reverb for both units
Combination machines on MM (FM with pulse or SID for example)
RAM machine/funtion on MM with, e12 style or other parameters
Slightly more powerful MD track preamps
Multi-band distortion
