I do not disagree with what you are saying but can understand why the rankings can be questioned. Even looking at my own school (Michigan grad) I question the rankings. When pubs put together lists of top research institutions we are generally top 5. When you talk grad schools generally top 10. Overall top 25 in the world. However, when rankings look just at the undergrad we slip a bit.
It is more than fair to say that things like research and graduate programs have little to do (only in select situations does it have a direct effect...indirect is a much longer discussion) with the undergraduate experience. However, if you are going to separate things to get a true ranking of the undergraduate experience you need to do it on a more apples to apples criteria. Michigan is not unique when it comes to this, but as a larger university, what separates it from many of the universities above it or around it (rankings wise) is the breath of programs it offers.
While I think it is great Michigan offers programs like Nursing, (The School of) Natural Resources (aka tree hugging), Kinis, etc. they all have their own admissions and the standards are below (in some cases far below) those of the core schools such as LS&A (Liberal Arts), Engin and Business. And in general many of the smaller universities only offer those core programs and are thus not weighted down (in the rankings). I'm not sure what percentage of the undergrad population is in those "outside" schools but it is enough to effect the rankings but at the same time does not represent the "general" student population (they have zero impact on the majority of undergrad students' experience and education) .
So my point wasn't to just say Michigan should be ranked higher...it is actually that the bigger a school is the more you need to start stripping away layers in order to get the real picture. And at least from a Wall Street recruiting standpoint (I've seen insider lists on priority schools) I think they do. I know Michigan is generally considered higher by them then what they are on the US News list...but here is one that might surprise you...PSU shoots up through the rankings...who would of thunk it (well I guess those who strip things down to the core did)...
You bring up great points, but as I think you will agree, at the end of the day we still have to use some criteria to rate schools. The points you raise invite skepticism as to the overall rankings used by many publications, which include, as you note, the rankings of the graduate school and quality of research.
I'm not sure all that a specifically undergraduate criteria would take into account, probably things like access to professors, class size, expense of education, average gpa, things like that. In any case, and you may very well agree given your comment about their "indirect" influence, it is foolish to focus on criteria that are disconnected from quality of research and graduate school rankings. One reason why is that top graduate schools tend to attract top graduate students who, assuming they are motivated to educate and not merely research (as I take it many are), will likely teach the material more effectively than a TA at a lower ranked school. So while professors at public universities may have little effect on the quality of a student's education, since it may be that they only interact with students perhaps two to three times a week during lecture, TAs can and do have a profound effect on the quality of the undergraduate experience.