Hi Scott, a friend here in Iowa has done that interior lake-hopping trip on Isle Royale and raves about it. FYI, it is better suited for a canoe than a kayak due to several portages, mostly short, but some long, wet, rocky, and steep. Those could be awkward with a kayak. Then there's the problem of carrying your gear, which consists of many small packages with a kayak instead of only a few big ones (carried backpack-style ala the "Duluth pack") with a canoe. This results in an extra trip or two back down the portage trail between the landings. On the other hand, you wouldn't want to do the Superior shoreline with a canoe unless you had absolutely calm water for the duration of that segment.

I'm originally from Michigan myself (Detroit area) and "discovered" the St. Clair Flats (a delta on the north side of Lake St. Clair, the "little" Great Lake) as a great kayaking place during a trip "home" a few years ago.