You'll get a little deeper bass extension and authority with the ProLogue Two, and perhaps a bit more detail, too. The ProLogue One has a lusher sound from top to bottom.
I prefer the ProLogue Two because it gives me more flexibility. Replace the standard KT88's with a quad of EL34's and basically you have a ProLogue One. Of course, there are other possibilities for tube rolling as well.
As far as I know, Stereophile didn't specifically pick the One over the Two...they just happened to review the One so that's what made it to their list.
I reviewed the Two for Positive Feedback Online three years ago; you can find the review in our archives at www.positive-feedback.com. For the record: I still have it and after three years of constant use it has been dead reliable. It's a rock-solid product.