I have camped all along that route. I have never followed it end to end in one trip.
Assuming you know about the Duluth end of the trip, then you know about the many water falls across northern Wisconsin. See Pattison State Park and/or several others.
There are endless campgrounds of all types over that route. Local roads are the best choices. Discover endless surprises and stop frequently to explore. It is a birder's paradise. Sittings change with the seasons.
The St. Croix river joins the Mississippi and is a great canoe and kayak wild river.
Wyalusing State Park where the Wisconsin River joins the Mississippi is a must see. Spend a few days.
Hike the bluff trail and canoe the back waters.
Fish and watch the eagles.
Rent a boat and picnic on a sandbar.
Check out Effigy Mounds Federal Monument on the Minnesota side (north of the bridge).
Also, Pike's Peak park on the Minnesota side (south of the bridge).
Historic Villa Louis is in nearby Prairie Du Chien WI. Take a tour.
Gamble on a riverboat on the Minnesota side.
There are endless small campgrounds at dams and small local and state parks. and lots of historical sites everywhere. Explore local side roads. Stop often.
Tour St. Louis, "gateway to the west". See the Arch from the inside.
There is a major archeology site just west of the city.
Of course New Orleans is at the south end, but you can drive out into the delta until the road sinks into the Gulf.
I wish you good luck and happy trails ahead!