I've been meaning to write some more impressions of how these compare, but here's a quick take.
Comparing the two as DACs, the Duet 2 exhibits greater extension, particularly in the treble range. Both seem to exhibit the same level of detail, but they're more apparent with the Duet 2. The original Duet sounds a bit smoother and the notes sound rounder while the Duet 2 is more analytical and true to the content. I never noticed any imaging shortcomings with the original, but the Duet 2 does seem to up the pinpoint placement factor to a noticeable degree. At the end of the day, they're both fantastic. Critical listeners should opt for the Duet 2 while those looking to just sit back and enjoy should opt for the original. I fall into the former category and, although I would still be happy if I kept the original, once I got to compare both extensively in-home I found myself wanting what the Duet 2 offered. To me it was a relative "upgrade," but since both are great performers it should generally be though of as a side-grade while some tastes may even render it a downgrade.
The application I would definitely recommend the Duet 2 for over the original, however, is if one intends to use it as a DAC/amp combo. The original Duet's headphone out is by no means bad, but the Duet 2's is leagues more expansive with a surprisingly decently sized soundstage, fantastic separation, punch (especially in the bass) that trounces the original, and a completely grain-free presentation. The fact that Apogee was able to coax so much performance out of such a small form factor is exceedingly impressive. It doesn't beat having a dedicated amp, but I could live with it as an all in one solution and do so with a smile on my face. :)