Its hard to go wrong on either side. I've ridden WI S to N and enjoyed it. As other's have posted MN will have more traffic and farther spaced towns, but I think it generally has a good shoulder as does WI.
You may consider if you would like the river and views on your right or left. I think the WI side may offer more camping options and is a little more quaint.
__________________
Nothing compares to the simple pleasure of a bike ride - JFK