The Finalizer 96K does several extra things compared to the MD2 like for example Spectral Stereo Enhancement, and Up & Down sampling.
The Multi-band compression is quite similar in the two units.
The MD2 package actually consists of two components: Multiband Dynamics and the Toolbox (stereo adjust, EQ, delay, fader, dithering). If you want to run these two components at the same time -- which is what the Finalizer 96K is capable of -- you'll need two DSP cards in your M5000 mainframe.
Additionally, the Finalizer can run its internal processing at 96 kHz. In the M5000, everything runs internally at 48 kHz.
For further details on the differences in parameters, please refer to this FAQ.