I went to marquette, but had plenty of friends that went to UW. So let's break it down.
MU pros:
1) Catholic University means strong philosophy and theology if you pursue it... it doesn't confront you with religion often if you don't look for it (I would have liked more of a religious presence on campus).
2) A premier basketball team in the Big East with a focus ONLY on basketball (no football) gives an electric atmosphere at the Bradley Center, the PRO venue where we play.
3) Very strong programs in Law and Engineering.
4) Smaller student population actually translates into smaller class sizes, especially early on. The only classes I had with more than 30 kids were intro classes for generic science courses that everybody has to take.
5) You will not be bored in Milwaukee if you put out even a small amount of effort. With the Kala Trava (art museum), college and pro basketball, pro baseball team, malls, opera, orchestra, public museum and zoo, plus university events, a nearby RAVE, and a short jump to Chicago, you're only bored if you guilt yourself into staying in and studying.
6) several close by hospitals if you feel the need to volunteer. As well as volunteer organizations on campus.
7) The campus is well maintained... expensively maintained, but well-done.
MU Cons:
1) the religion thing for me.
2) No pro football
3) As a chemistry major, the chem department was very small student-wise (I was one of 3)
4) The Med College of Wisconsin is historically related, but only historically... no favored admissions link between the two.
5) Occasional brewery smell in the mornings is not a good smell when you have a hangover... but is fondly reminiscent if you're not.
UW Pros:
1) You live in a college, so everything is focused on the university.
2) Having gone to several UW football games, there's nothing like a good tailgate in which everybody is partying on their lawn before moseying over to Camp Randall Stadium.
3) Good football & basketball teams in the Big Ten. And as my sister's say, Bo Ryan is so cute.
4) Since UW owns their med school, they have direct admissions programs where they guarantee admission if the student performs to a certain level... (year early too?)
5) Larger student population and cheaper since it's a public university.
UW cons:
1) UW is one of the most liberal campuses in the nation if that's a problem for you.
2) Class sizes are very large until upper level classes and graduate work.
3) Less to do in the city outside the university and the nearest major city is Milwaukee (vs. chicago)
4) No major religious presence... though you can involve yourself if you look for it.
5) Alternates with the University of Colorado for biggest partying university. If you don't go out for Thirsty Thursdays, you will likely be an irregularity.
Hope that helps. Just remember, at every level, you determine your own success. The opportunities are there to succeed to the degree you want to at both universities.