Thanks for the replies.

Thanks for the correction on the NEX schedule. It appears I was looking at the NEX schedule that showed which departures had the new trains that are being introduced in stages. I'm still inclined to take the NEX to Tokyo Station (not sure why ChrisLi mentioned Shinagawa station in the first reply; is it closer to the Conrad?) and then cab it to the hotel. I'm not a big fan of two hour bus rides (done my share ex NRT in the past), and I also figure my kids will be more comfortable on the train versus the bus.

Unfortunately, I already booked the flights, so I can't easily change the tickets easily. When I booked the tickets, I wasn't planning on visiting Hakone. Of course, the train to Kyoto makes a lot more sense if we were already going to Odawara from Tokyo. To eliminate the backtracking, I might decide to skip Hakone on this trip and save it for a return trip. Odds of seeing Mt Fuji in July are low anyway. Or, is Hakone a must see? I was pretty positive my kids would enjoy the toy train and the outdoor art museum. Oh well.

Instead of Hakone, what about a day trip to Kamakura? What's the best beach around Tokyo? Any other good (easy) day trips ex Tokyo or Kyoto/Osaka?

Thanks for the Kyoto lodging suggestions. I'm still looking, but unfortunately, I've also concluded that I can't stay at a ryokan (or for that matter to a kaiseki dinner at Kikunoi) with the kids. Better to save that for a weekend trip without the kids one of these days. The kids are not going to be a problem on trains and planes, but they would be out of place somewhere with paper thin walls.