We did 4 days at TDR and 3 days in Tokyo and then headed to Osaka/Kyoto for 7 days.
We stayed near Disney the whole time in Tokyo, but we are a family of 5 and it was significantly cheaper for us to stay in one of the large family rooms at the Sheraton Grade Tokyo Bay then anywhere else. It was slightly inconvenient but not horribly so. We ended up taking the free shuttle to the Manheim station most of the time to save a bit of money, which again was fine for us. One night it was kinda late coming back from Tokyo so we just used the bayside station. We may be back in Tokyo for a few days and we may or may not do Tokyo Disney Sea for one day and we are considering staying at the same hotel because we liked it well enough. It would be nice to stay closer to Tokyo, but at most of the Marriott hotels we would need to get 3 rooms which adds quite an expense and We are platinum with Marriott so like to stay there for several reasons.
We did do the Robot restaurant. Dh and 2 of my 3 kids (13 and 9) loved it. My 15 year old and I thought it was okay, something we were fine enough with doing once but wouldn't do again.
For the second part of the trip we stayed at the Courtyard Marriott that was just outside the Shin Osaka station, it made daytrips to Hiroshima and Nara really simple. We did a 7 day Japan rail pass for the second half of the trip. The first part in Tokyo we just used Sucia cards and paid for the trips that way. We didn't feel that they 14 day pass would have been worth it for us. I'd have to do the math to see if it was a good choice or not, but it worked well for what we wanted.
Anyway here was our basic schedule
Day 1 Arrive in Tokyo, Tokyo
Disneyland until we were tired, around 6pm
Day 2 Tokyo DisneySea
Day 3 Tokyo Disneyland
Day 4 Tokyo DisneySea
Day 5 Tokyo- Fish market (The new one had just opened), Harajuku street,
Day 6 Asakusa, Tokyo Skytree
Day 7 Samurai Museum, Robot Restaurant
Day 8 Train to Osaka, Ramen Museum
Day 9 Kyoto Sumo match, visited the Golden Palace and Gion district
Day 10 Nara day trip
Day 11 Osaka Castle, shopping in Osaka, Pokemon store
Day 12 Hiroshima day trip
Day 13 Kyoto bamboo forest, some shopping and another temple
Day 14 flew home