HomeSteak unless you’re there for 10+ days I’d suggest decreasing the number of cities, or changing a few to be day trips. Far better to spend more time per city!
The trains are great but it’s still a lot to navigate some of the larger subway stations (in Tokyo, Osaka, etc) and hotel check in can be challenging. You can stay in Osaka and easily do day trips to Nara and Kyoto.
That said, I really liked biking around Kyoto as it has a great canal. I would also highly recommend a guided tour of a temple/garden in Kyoto.
Holler if you want any tips.