We just did portions of your trip this fall. I notice you took Custer State Park out in your last itenerary. We're hikers and bikers, and Custer was one of our favorite parts of the trip. Its beautiful and so much less crowded than the national parks. Harney Peak trail is awesome. We camped at Stockade North - it was great.
Badlands can be done in a day. We spent one night there and did all the short hikes, as well as the ladders trail.
Staying in 2 different areas of Yellowstone is a good plan. Up by Gardner is a good location for touring the north. Fishing Bridge is a good location for seeing Old Faithful area, and the falls area. Fishing Bridge Campground is awful, but hopefully you are just using it to sleep. We stayed a week and thought it was too long. We both got tired of the crowds, and had seen enough thermal features after about 5 days.
We thought Colter Bay was great, but we lucked out with a really really nice site. The Tetons are beautiful. This was probably my favorite part of the trip.
I agree Estes Park is a tourist town. Didn't float my boat. The Rockies are amazing, but very crowded. As most places we went, once you hiked a mile in, the crowds thinned out considerably.
The hard part of advice is everyone likes something different!
Enjoy making those great family memories!