I've basically done this, but NRT-ITM instead of HND-ITM. Even NRT-ITM, though (which you'd think would be more of a clearcut choice), isn't really all that pleasant. It doesn't save any time and that bus ride at the end is just horrible after two flights like that.

That said, it's really six of one, half a dozen of the other. Both train and plane have their pros and cons. I remember that second flight being one of the weirdest flights of my life - I just could not get my bearings, and thought we were spiraling up and down the entire way. I also ended up leaving my jacket on the plane because I was so disoriented and had to go back to the airport to pick it up. And the bus ride was just a blur - I barely remember it, except for it seeming very long. But the train trip would have been more stressful at the head and tail ends, but less stressful in the middle.

Part of it depends on where you're staying in Kyoto. We were staying literally right next to the train station and I remember wondering why we didn't just take the train.