As a resident at UW-Madison that was a med student at MCW, I can tell you the following:
MCWs clinical experience is, in my opinion better than UWs. There is a lot more autonomy for med students in Milwaukee and you really learn clinical medicine well. Many of UWs medical students are farmed out to small areas throughout the state. This may be a positive or a negative depending on the person. MCW rotates through many hospitals in Milwaukee with the opportunity for rotations in other parts of the state, but only if you want them.
The didactics (first two years) of MCW med school was in the block format (and still is). Classes may be heavy in hours, but there is a great note-taking system so you don't go unless you want to. I chose not to go to the majority of my classes starting second semester of first year. I would basically take two weeks off after exams with little studying then start studying for the last two weeks before exams (for me it was mostly the last week). Overall I would rate the lectures a B-, but I don't know how UW lecturers compare.
As for cities. Madison is smaller than Milwaukee, but seems like it would have been a great town to be a med student in. Milwaukee has more variety of places to go and things to do and was a fun town overall. I'd say the town is a toss up depending on if you're looking for a college feel or a bigger city feel.
The reputation of UW is better than MCW, mostly based on the research done at UW. There are ample research opportunities at MCW as well, just not as well known or funded as a graduate research powerhouse like UW.
Good luck.
