The best attraction between Denver and Topeka is the Kansas Cosmosphere & Space Center in Hutchinson, Ks. Unfortunately it's 65 miles south of the interstate. It has the largest collection of Russian/Soviet space artifacts outside of Moscow, including Sputnik 1 and 2. They refurbished the Apollo 13 and Liberty Bell 7 spacecrafts here and have them on exhibit. It's a world-class museum and we try to make it there every few years.
I've never even considered stopping at the prairie dog place, it screams tourist-trap!
Science City was always been one of my kids favorite places to go when we would go to KC. Lots of hands-on activities for the kids and so much to do we usually ended up running out of steam before we saw all the exhibits.
If you stop at the Cosmosphere then I would recommend staying a night at Hedricks Exotic Animal Farm. We went there for a weekend and had a blast! We didn't do the Cosmosphere but wish we had. We plan to go back. They are close enough to do both. We stayed in the Pride of Kansas Suite.
http://www.hedricks.com/