Spent time training in both places, so I feel obligated to respond. As had been said, it's a matter of preference. Ann Arbor will keep you plenty busy & is a lot of fun in your early 20s (bit less so in your late 20s), whereas Baltimore is more diverse, cosmopolitan, but also rough around the edges. Not to be missed, is the proximity of B-more to DC and Philly, eastern shore (beutiful area, reminiscent of mid-mitten Michigan) and western Maryland for mountains & lakes. All with an easy short (2 hours or less) drive. For Ann Arbor you have Chicago (4 hours) and Toronto and to a lesser extent Detroit -- different choices, but just more effort getting there.
Yes you can benefit from a wider patient population in B-more, but you will also rotate thru the VA in UofM, you can volunteer locally (say an evening a week at a free clinic during your PhD) or choose to go to Detroit or its suburbs. The hospital facilities, general environment and personal safety/property crime is just much better in Ann Arbor.
Yeah, technically Hopkins is more prestigous but if you are looking at top 10 USNWR, the benefits thereof are minimal (& potential at best). The upside of prestige is my impression of Hopkins med students are uber-motivated/somewhat more intense. The attendings at JHH on average are also a bit more intense, again a double-edged sword.
I wouldn't worry about the size of your medical school class or curriculum structure AT ALL. Not important in the least. If anything, I would think about the size of your MSTP cohort, those are the peeps you will spend 7-9 years with and hopefully can make some life-long friends. Not much of an issue with either UofM or JHH, more of a concern when choosing a small program (anything less than 5 per year).
Last, but quite important is what is your PhD area of interest and do you see several (i.e. at least 3) potential mentors? Your PhD mentor may be the 3rd most influential in your life, behind only your parents and spouse. My gestalt is that in genomics/bioinformatics JHH may be superior, whereas Michigan does quite well in CMB, Physiology, Biochem, exercise physiology. That's not to say you won't find a fantastic mentor at either place, regardless of your choices and your choices will change. Coming in, I was set on doing channel work/pharmacology whereas another individual within my MSTP cohort was set on transcriptional regulation/bioinformatics, and within 2 years we flipped based on interests/needs of our research projects. To some extent, same thing will happen with your post-doc.
On that note (& I come with my own biases) doing the loooong haul of MSTP at a more supportive environment, then matching a more prestigous/intense institution for a shorter, sprint-like residency may be the best bet. PM me with any questions.