I think the contrast between the two units is pretty simple. The USBPre2 is definitely the superior unit when it comes to raw sonic performance. It has all around better specifications, so if you're recording mosquito farts it's clearly the better choice.
The Mixpre-D has a better feature set for "professional" work, which is to say that most features were implemented with the mindset of working in difficult environments and interfacing with other professional equipment. Examples include AES digital output (and lacking SPDIF), 10-18v external powering via a hirose connector + internal AA batteries for backup, and input transformers for noise isolation.
Both are great units, but in my opinion the USBPre2 is theoretically the better unit under perfect conditions. I'm not particularly fond of USB powering and would prefer a locking power connector and the ability to use internal AA's is nice, but do prefer the better noise performance, SPDIF compatibility, and ability to sync to an external clock source.