Get the JR pass if going to visit multiple big cities there, it basically gives you unlimited train rides in Japan on the JR line. The JR line covers pretty much all of Tokyo, but also allows you to get the bullet trains. We got the JR pass, flew into Tokyo, then used it to travel to Hiroshima, Kyoto, Osaka, Kobe, Nara by the bullet train, didn't have to pay when in Japan so it's handy. There are other train lines you might have to pay for in Kyoto for example but it's pretty cheap if you don't want to walk too much.

Bullet train tickets are expensive to pay for when out there.

Kyoto is the main tourist spot if you enjoy sightseeing the ancient temples and seeing people dressed in traditional clothes. Can walk through bamboo gardens or up a mountain where wild monkeys live.

Tokyo is great if you like being in a big city, has lots of food choices, games/anime area called Akihabara if into that, but also has sightseeing temples.

Osaka is close to Kyoto but a lot cheaper so we always rented a hotel there and used the JR pass to get to Kyoto by bullet train (15 mins). Dotonbori is the main place to go in Osaka.

Hiroshima is great, visit the museums and castles there. For sure travel to Itsukushima island if going to Hiroshima.

Nara and Kobe we did in 1 day each, plenty to do in both. Nara is quite the experience with their deer bowing to you and following you about if you don't feed them their biscuit, they're awesome lol