I have an 11 yr old son and visit somewhat regularly. Never heard of the Nikko thing although we're always riding Tobu. Sounds cool.
I'm sorry to not hear any mention of Miraikan or Sony Museum while you were in Odaiba. A few other things that might have been cool would be walking along Ameyoko, Tsukiji (recommended first day with the jet lag), maybe Shibuya, Roppongi, Ginza.
Sound like you had a wonderful time!