I believe there's a place in KC called The Great Wolf Lodge, sounds similar to the one described above--indoor waterpark, hotel, restaurants, etc. Of course you'll also have Worlds of Fun/Oceans of Fun in the KC area too.
Also recommend St Louis--6 Flags Amusement Park and Water Park. You must get some frozen custard at Ted Drewes if you go to STL. Seriously. They also have an awesome City Museum, not sure if the kids would be old enough though. I was fascinated when I first went when I was 17--it's 100% interactive, with things to climb on or through, puzzles, games, funhouse, and most of the displays are fully recycled products. I remember going outside on one of the top levels and crossing a bridge made completely out of old wire farm fence, and in the middle was a gutted-out old helicopter. You have to be there to believe it and do it. Just checked the website, ages 3+ are $12.
Ozarks?
6 Flags Chicago?
Black Hills?