There really isn't any way to avoid a lot of mountains, you can stick to Interstates as much as possible since the grades are limited on the Interstate system. Colorado is nothing but mountains in the area you are going to. And Yellowstone is at 9000 ft.
For only two weeks you may want to rethink this path you have. You will be spending almost all your time driving. Maybe substitute Rocky Mountains NP for YNP. And drop Rushmore, an hour at Rushmore was plenty for us.
You are going to driving right by dozens of major attractions and it's hard to list ones that you may want to see.
