Between Tokyo and Osaka, Shinkansen all the way.

The HND-ITM air trip is only a hassle. Making my way to HND, riding that crowded Tokyo Monorail, going through security, boarding, waiting for pushback, take off, only for what, less than 30 min in the air, only to land at ITM, taxi to gate, deplaning, collecting luggage, then taking transit to Osaka city center...ugh.

Shinkasen is more straightforward: board, off you go, fire up laptop, arrive at Shin-Osaka station.

I'd say the same for others like Tokyo-Kyoto, Tokyo-Nagoya, Tokyo-Sendai, or Kagoshima-Fukuoka; Shinkansen beats air travel hands down on such distances.

OTOH, on certain places where rail doesn't make sense (yet), I'd fly. For example, Tokyo to Kanazawa. Until the Shinkansen gets there, HND-KMQ is still my preferred route. Others like HND-CTS or HND-OKA, the only option is to fly.