I've got both of them and while it's true that the C variant is the newer sim product, the plane itself is the older variant so the C has a steam dial cockpit while the D has a glass cockpit.
The PMDG C has three variants for passenger, freight and freight with extra hold under the fuselage models. The VC for both C & D is fairly similar to be honest so if you're going to get one I'd say stick with the D model as I'm pretty sure the EHM repaint won't fit the C model (although you might be able to if you're familiar with texture files).
As far as flying goes they are both nice planes, there's certainly nothing wrong with the flight model of the D, in fact the only thing that goes against it is that the panel is fairly rudimentary compared to PMDG's other planes - it uses some default gauges from the King Air. That said, for the price, the D is an excellent buy.