Educational assessment is extremely difficult, and I certainly don't have any answers on that.
But trying to predict a graduation rate based on student profiles and then using that to assess how good of a job a school is doing seems ludicrous to me. If a school overperforms the prediction, I see two possible reasons for that in general (assuming that predicted number actually means anything):
1. The school has a positive effect on the students to help get them through to graduation...fostering student happiness, being proactive about academic issues through a helpful and supportive faculty, etc. This is what U.S. News wants to capture.
2. The school focuses on doing whatever it takes to get a student to the diploma. Lower standards, grade inflation, etc.
I'm sure U.S. News is trying hard to focus on #1 by including other data that should be indicative of a quality education, but there are multiple ways to get to an "overperforming" graduation rate.
Schools like Harvard and Stanford have long been notorious for grade inflation...once you're in it's nearly impossible to get anything lower than a C. They've been trying to combat this a bit, but I remember maybe ten years ago when it was revealed that something like 90% of Harvard students were graduating with honors. Yes, most of them were very smart to get in in the first place, but Harvard professors should also have higher expectations.