To be honest with you, I would have found this a difficult question to answer up until my current rotation, because we each only have the experience of our own institution until we start doing electives/away rotations, it's hard to know what you're missing out on or where your school has been exceptional. For the first time I am at a site predominately used for training students from another program, and it has brought to my attention the following:
1) How many if any rotations do you have to do outside of your school's home institution? Are you going to an academic site for those? A place that has residents and other students? Some schools seem to send students wherever they can, which sometimes means mediocre small hospitals with low patient volume, less interesting cases, physicians who are not really committed to teaching and/or are relatively inexperienced in how to teach. While going to a site without residents can be good in certain circumstances (i.e. an attending might let you do or assist procedures that would normally go to an intern/resident), it is easier to escape with a lot less teaching -- there's incidental teaching that happens even from having other med student peers around you.
2) What type of care do your teaching hospitals provide (especially for internal medicine)? Do attendings make sure that students only follow patients with educational value? I've now met students who have done all of their IM rotations in a long-term rehabilitation hospital. Their entire IM education has been based on patients, such as those hospitalized for long term antibiotics b/c they can't go to a homeless shelter with a PICC, that my school deems to have no educational value (and moves to non-teaching teams without residents/students). Patients at rehab hospitals (and to some extent smaller community hospitals) only have stable issues and arrive with an all but complete assessment/plan from outside hospitals, so it's difficult to develop good physical exam skills, to learn fundamental guidelines and diagnostic criteria, and to learn diagnostic thought processes that become second nature in the acute hospital setting. They also have not developed the same skills for rounding and following patients, b/c the pace is so slow, and I expect it will be very difficult for them to transition to being a resident.
3) Related to 1 & 2 . . . how do they cover Pediatrics and OB/GYN? If you want to do pediatrics and want to practice as a hospitalist or in an academic capacity, you probably would be better off at a school that does not do all peds in community outpatient clinics. Similarly, if you want to do GYN, you probably want to make sure you get surgical exposure on your rotation, b/c sometimes you go out to the community and do tons of OB and pap smears but have no time in the OR aside from C-sections.
4) Which rotations are required, when can you take them, and how is the schedule decided? Some schools don't require neurology. Some don't require emergency medicine. Some have different #s of weeks of surgery required. Is the schedule done by lottery? Do they help students who get screwed by the lottery -- like if you're a budding surgeon and get assigned to surgery as your first rotation when you are totally lost and won't be able to get a LOR, will they find a way to move it to a little later in the year or do they just say it's tough luck? Is neurology (or some other rotation) stuck in the 4th year such that you may not be able to take it before picking your field for residency?
5) What percentage of clinical rotation grades is determined by your shelf exams? Shelf exams are like mini board exams at the end of each rotation. At some schools you have to get above a certain score to pass, but it's not factored into your grade. At other schools, it's factored in as a certain percentage. Shelf exams are scaled to an average score of 70, I believe, so if it's factored into your grade for the rotation and 70% is the cutoff for passing your rotation. . . you can do the math.
6) How are didactics and shelf exams administered in clinical years? Evidently a few schools squish them together into chunks instead of doing them with their respective rotations -- so do you have all of your lectures for the next 3 rotations in a week-long block versus during the pertinent rotations? do you take shelf exams at the end of each rotation, or do they make you take multiple ones in a day/week between rotations?
7) By what date do you have to take your Step 1 and 2 and can you get time off if you need it to prepare for either? How much?
8) Are the 4th years happy with the advising/logistical accommodation of the residency applications and the interview season? This is a question you probably should ask directly of a 4th year student. Do students feel like they are limited in any way from going to their interviews? I doubt this is typically a problem, but I've met a few people who are assigned at their school to mandatory portions of a rotation during December when I'm free to go on my interviews. How is the quality of advising for the residency application process? (This can be surprisingly bad at some institutions). Do they leave you to figure it out for yourself, or will they tell you all the important real (and unofficial/recommended) deadlines? Do they advise students on what type of LORs are needed to make sure they satisfy the req's at all of a field's residency programs? Do they tell them how many away rotations should be done for the field they applied to? Do they set them up with field-specific advisers or is there for instance just a non-MD counseling everybody going into any specialty?
9) Grading system and how if at all do they rank/compare students? I wouldn't want to go to a school that gives out "low pass" or at least I'd want to verify with students that it wasn't common to receive. On the dean's/MSPE letter that goes out to residency programs, all schools have a way of comparing you to your peers -- whether it's an adjective, class rank, or quartile. I don't know what's most common, but I wouldn't want to be ranked.
10) Process for addressing student mistreatment by attendings/residents promptly? Do they collect feedback on this and is their a positive trend? Do students feel like they could report something?
11) How often do students get dropped from required rotations last minute? This should be ~never.
Some of these questions will be overkill for schools that have a good reputation established, but if you have any inkling of concern (such as with a new program), I'd find out all of these things before accepting admission. Obviously at an interview, you don't want to be severely negative -- so some questions are better addressed by investigating, asking non-interviewer students, reading online, etc.