I think it depends on your preference. Location wise, Chicago can definitely give you advantages in terms of opportunities (internships, rotations etc) but it is recently named the most dangerous city in America. <Reference:
http://www.washingtonpost.com/blogs...ago-passes-new-york-as-murder-capital-of-u-s/> (and even besides this data, many parts of chicago is dangerous not only to mention one of the highest living costs in America.) Madison is a great city and I definitely love the atmosphere there but definitely way smaller than Chicago.) School wise, I believe Wisconsin-Madison is generally a better school. (better university hospital and medical school). I don't know the difference much between the two in terms of pharmD program, so I don't think I can help you with that. Hope this helps...somewhat l0l