I don't know that there's any difference in the electronic components used on the boards. (Both Ultra versions use Burr-Brown OPA627s, for example.) I suppose it boils down to space issues, connection inputs, and DAC options.
The desktop offers full RCA jacks on the back and an optional, integrated DAC with 3 of its own connectors (coax, optical, USB). You can also upgrade to a stepped volume control, which I suppose will offer a firmer feel, a more stable presentation.
The micro uses 1/8" jack inputs and as far as I remember requires an outboard DAC for that functionality.
So if like me you're connecting full-sized components and have headphones with dedicated 1/4" jacks, go with the 6" x 6" desktop. If you integrate the DAC, it's one less wall wart and set of outboard connections to fuss with. Plus the larger form factor makes it easier to reach and use the switches.
If you're connecting a portable mp3 player or laptop, space is at a premium, or you want somewhat greater transportability, go with the 3" x 3" micro.
I have the Desktop Ultra and dedicated Power Supply. I wept like a grandmother when I tossed my billfold to the moths for it. It's given me nothing but smiles in return. I feel no need whatever to trade to anything else.