Hi --
I am a student at Northwestern / Feinberg, so I just wanted to take a moment and respond with an admittedly biased perspective but one that at least has the weight of some experience behind it. First off, you are dealing with what we like to call a "first world problem." These are both excellent medical centers with fantastic faculty and world-class facilities. You really can not make a wrong decision. I interviewed at Michigan and wound up going to Northwestern for medical school and I really think very highly of both places.
To address some of your questions:
Prestige: Obviously I am biased here but I really do not think there is any difference between the two medical schools in terms of prestige. That being said I want to emphasize that prestige really matters when it comes to the residency selection process, but if these are the two schools you are looking at then you really do not need to worry. If you think of medical school from a practical standpoint the goal is to match into a residency that corresponds with your desired specialty (first and foremost) and match into the program that attracts you. To that end most of my classmates have received interviews to incredibly prestigious programs in a variety of medical specialties. Yes, there are a few people each year that are unhappy with where they match at Northwestern and there are a few that are simply told not to apply into __________ (Dermatology, Plastic Surgery, Orthopedic Surgery, ect.). That being said the people that do utilize the career counseling at Northwestern are very happy with the interviews they have received and the majority of classes in years passed matched into competitive programs all across the country in a variety of specialties. If you are from the Midwest and think you might want to stay there for residency both names -- Michigan and Northwestern -- will help out when you turn in your residency application. I would not worry too much about this.
Cost of Living: Yes, there is no doubt Ann Arbor is less expensive than Chicago. However, if you look at housing carefully you might be surprised at how close the cost of living really is. You do not need a car in Chicago, and if you move away from the medical school just a few miles and endure the "hardship" of a 20-30 minute commute you really only pay a few hundred more per month for housing in Chicago. If you factor in the cost of owning a car that narrows the gap even further. By the way, Northwestern tuition includes access to public transportation year-round.
Flexible Third Year: I can not speak to Michigan's schedule and if you liked it that is great, but I will say that there is a ton of flexibility at Northwestern during your 3rd and 4th years. They essentially give you about 4 months off and you can use them whenever you like -- during third or fourth year. Also, if you do research during your third or fourth year, which about 95% of students do, they give you credit for this and they are very lenient on the hours you have to work. Most students do clinical research using their laptop while on the interview trail. A few hours in a Starbucks here, a couple of days spent back in Chicago working with your advisor, and you have a paper under your belt and 2-6 weeks of research credit. Michigan's curriculum may be more flexible than Northwestern's but I can assure you the Northwestern curriculum is more flexible than most medical schools.
Large Urban Environment: You will definitely treat many underserved patients and you will definitely see some things in the ED or on acute care surgery that you would not see in a rural setting if you go to Northwestern. That being said the volume of gunshots, stab wounds, and even car accidents has really diminished since the University of Chicago (also a great school) opened its level one trauma center. If trauma excites you you can always do an away rotation at Cook County hospital during your M4 year wether you go to Northwestern or Michigan.
Friends and Family: I do not care who you are, if you are reading this post never underestimate the importance of a social network outside of the medical school. I do not think taking the train or driving between Ann Arbor and Chicago would be an enormous barrier, but I will say that medical school is very, very difficult and you having a friend that you can talk to about something other than the internal medicine shelf or step 1 is a real asset.
I hope this helps. There is a lot of misinformation out there about Northwestern which is why I wanted to respond to your post. Yes, it is not a perfect place by any means but some of the things I have read online are just false. It does not have a cut-throat culture although every medical school has a few "gunners." The patient population is not all rich people pulling into the hospital in their Maseratis although there are some patients who fit that description. The faculty and the residents are, for the most part, very nice and supportive although there are always a few egotistical jerks in any academic medical center. The facilities are absolutely amazing. That being said I think all of this is probably true for Michigan as well. For anyone making a decision like this I will say go with your gut and if the school offers a "second look" take them up on that. Also, take everything you read on Student Doctor Network with a grain of salt. That includes this post!
Best of luck.