For a 3 month trip, I'd get a map of the USA and simply mark all the spots that you are interested in visiting. (even if you go a little crazy with this, that's OK). Then after you have all the spots identified on the map, draw straight lines from one to the other and when done, look at the spider web. See which is the best route to travel to comfortably accommodate as many locations as possible in the time allowed. This will give you your basic route.
Then begin fine tuning everything. Start with the route from "home" to point A. Do research on the internet for things to see and do, and experience, to eat, sleep, spend the night, visit, or whatever. Write it all down. Now do between Point A to Point B and do the same. Go through the entire route and when done, look at the complete list of everything. Now, pick out the best of the best and eliminate everything else. This is your big-picture plan.
Now, when actually on the road, if you plans change "on the fly" there is nothing wrong with that. Plans can change drastic hour-by-hour. Adjust to what really interests you and how tired you become. You may find you really enjoy a specific location. If so, then there is absolutely nothing wrong with, even hanging out a month at that one spot. The important thing is to be flexible and make the trip meaningful! It's not able miles, or how many destinations you can make it to, or how much you can squeeze into a specific time line. What is is about is having fun. AND the JOURNEY should be as much fun, or even MORE fun than the DESTINATION. The important thing is to make your 3 month trip meaningful to you and your spouse! That's all that really matters. Enjoy the trip!