Yes you stop off at the cities mentioned but when travelling between them you visit many small traditional route 66 towns, meet some charactors, a few museums, diners, etc. Yes most of the journey is on modern highways but thats because a lot of the origional road isn't there, in parts you do go along the origional road.
You need to phone JY and ask about discounts if you arrange your own flights, i know a couple of people in our group did this.