I used a pocket wifi with unlimited data, it worked great. Of course you can get e sim cards, but I mean if I'm using my phone most of the day I didn't want to take the chance of using too much data. One less thing to carry though if you don't go that route. At the same time, pocket wifis are usually very small. The best tip I can give is to download a local version of the Google map to save you a ton of data. Otherwise you may literally end up using 1gb+ just to download the map everytime.
For flights, if you're willing to pay extra, premium economy ANA is completely worth it. The flagship lounge in Haneda and the extra comfort is well worth it. Also, if you book through ANA make sure it is an ANA operated plane. Some ANA planes are operated by united and are the same price for vastly inferior service.
Also absolutely take the shinkansen, it is way more comfortable than flying, and it's easier.