Minnesota and Wisconsin are both top-notch for ChemE. I don't think there's really much of an academic difference.
Having visited both schools with DD, I can say that we left UWisc unimpressed. UMinn has a better program, a new Nanotechnology & Physics center to be completed in 2013 and in our experience, more hands on opportunities. UMINN's honors college appears to be an amazing opportunity if you are interested/qualified for it.
More importantly, Minnesota claimed the 2011-12 McNaughton Cup and advanced to the Frozen Four. Wisconsin? Does the phrase 'losing record' ring any bells?