I feel like we ended up giving short-shrift to Tokyo, but my kids would have happily spent more time at TDR. Our trip breakdown was:
Arrived Sunday afternoon, quick evening visit to toy store in Ginza
Monday morning -- trains to Hakone, arrived Gora mid-afternoon, did the Hakone open air museum
Tuesday -- Hakone round-course
Wednesday to Saturday morning -- Kyoto temples, with a day trip to Nara
Saturday -- bullet train back to Tokyo, overnight in Shinjuku with Robot Restaurant visit
Sunday -- Tokyo Metropolitan building, Shinjuku Gyoen garden, headed to Maihama
Monday to Thursday -- TDR, stayed at MyStays Maihama
Friday -- transferred hotels to Asakusa area, Kappabashi street, Sensoji temple
Saturday -- Edo Tokyo museum, airport