The only con I know with the Desktop, and the sole reason why I opted for the key version instead, is that it's not readily rack-mountable like the Prophet 08. So I don't think they have cut any corners, size-wise, to cram everything in.
I can relate to your reasons for getting the desktop instead, when playing live and wanting to bring enough gear for ones arsenal, the footprint is important as to what gear I actually end up bringing or not. Rack is preferable when possible imo, for safety, ease of transport and being able to bring the most gear relative to footprint, and the instruments are less "exposed" to potential harm. There's just too many knobs on the Rev2 to fit into a rack module it seems...