Frankly I-90 is not my favorite route; it's generally quick and direct, but not always the most interesting. I might consider a more northerly route (at least in part), perhaps going across Ontario from Niagara Falls to Sarnia and then across the lower peninsula of Michigan to the SS Badger--which is unfortunately not inexpensive--and find my way to route 2. But that's just my own preference, nothing more.
If you do go along route 2, Havre, MO has a fascinating underground tour.
Some ideas that haven't been mentioned yet, in no particular order:
The Henry Ford (aka Henry Ford Museum and Greenfield Village) in Dearborn, MI. Two full days would not be too much there in my opinion.
Seabreeze amusement park (near Rochester, NY) is a neat little traditional family-owned amusement park.
Letchworth state park is fabulous. Watkin's Glen is also a lot of fun but a little more out of the way from I-90. Not super far from Watkin's Glen is the Corning Museum of Glass (in Corning, of course), which is a good it better than it sounds at first.
Chicago has many great museums, etc., though getting to them while traveling by RV can be rather a challenge. Among them, the Art Institute should not be immediately discarded; there are things there that appeal to kids as well as adults.
The House on the Rock in Spring Green, WI sounds...well, unique, to say the least. I have not been there myself. I would like to experience it at least once at some point, but quite possibly once would be plenty.
I did very much enjoy the badlands a lot when I visited with my mom as a 10 year old (I think--I might be off by a year). Theodore Roosevelt NP has similar terrain, too, and great (nearly guaranteed) viewing of prairie dogs and bison, among other wildlife.
Paul Bunyan Land, in Brainerd, MN sounds nice to me. I haven't been there myself, however.
(It's very much out of the way, but the St Louis City Museum is amazing, particularly for children and children at heart. It's more a playground mashed together with an art installation than a normal museum. There are a number of other great things to do in St Louis, as well, such as their zoo and the arch.)
