The basic question is where you'll be a happier MSTP student. Here are the specific factors I'd consider:
1) Medical School - As most of us are planning for careers in translational research, our clinical training will be of an utmost importance. With that said, you will have a definite advantage at Michigan. As I'm sure you are aware, UMMS is consistently in the top ten for the US News Research rankings. But even more than this, the quality of the affiliated hospital in Ann Arbor is far superior to that in Madison. The UMich Medical Center just has superior departments in a wider range of disciplines than Wisconsin. Also, the patient population and range of clinical experiences would be more diverse. This might not be as important during the basic science years, but once you start hospital rotations (and are considering what in the world to do in that next phase that is residency), the value of such strong clinical departments is, well... priceless.
2) Doctoral Research - When it comes to the Ph.D, it is my opinion that the department is not as important as the individual P.I. with whom you complete your research. It only takes one [lab] after all. The question at this point is whether there are faculty whose research interests sound promising to you. The two or three lab rotations we do are there to help us determine whether the environment is right or not.
Madison does indeed have a higher rated biochemistry department. But is that the be-all/end-all? Another consideration is the strength and overlap of those labs affiliated with the medical school. For example, Ben Margolis and Sean Morrison are both U of M HHMI Investigators that are doing interesting work in cell signaling and the mechanisms of stem cell regulation, respectively. There are probably a host of other faculty at the U of M medical school who are also doing work that might be of interest to you. I don't think the same can be said for Wisconsin, where the graduate and medical school might be more stratified. And since a stated purpose of the MSTP is to produce physician-scientists that bridge the gap between basic research and clinical practice, this is something to consider.
3) MSTP Students - What are your impressions of the students in each program? You will be spending quite a few years with these people, so with whom were you more comfortable? One caveat is that there are programs where a higher proportion of the students are more apathetic to their research (i.e. the Ph.D is more of a title to tack on after their names more than anything else). Here I think it is important to differentiate between the individual doubts/ambivalence that all of us undergo during this long process, compared to a more general underlying indifference that is apparent in many of the students encountered.
I personally think it adds a lot when the students are genuinely dedicated to their research. They challenge us, and contribute to our growth as physician-scientists. You will find such individuals in all MSTP programs to be sure. But the difference in overall mentality and environment between programs are observable and should not be discounted, especially when considering personal happiness.
Well, those are some factors I think might be worthwhile to consider. I would lean towards Michigan myself (Wolverine football notwithstanding!). Either way though, you have great choices. I wish you the best of luck.
