Excited and a little overwhelmed

My daughter and I are coming to Japan October 16th, beginning and ending in Tokyo (Narita) . We will be there for 17 days and will go to Hiroshima from Tokyo then to Kyoto, Nagoya (for Studio Ghibli Park) to Hakone then back to Tokyo. Lots of moving around and wanting advice on the best options. We will need the fasted way to Hiroshima from Tokyo as we will spend one night there and want to have the most time we can each partial day. We are considering the Green Class but not sure if all routes will have that available and if is is worth it. Thank you for your consideration on our trip.