We did Japan on a self guided tour organized by Inside Japan this past December. I'm going to agree that there is sooo much to see and do in Tokyo that trying a one size fits all approach for a large group is probably doomed to fail. It's too bad
ABD can't help you arrange your OYO activities, given the cost.
Consider looking at Inside Japan's itineraries. That will at least give you more ideas about what it available.
It is VERY easy to navigate the train/subway system there. Google maps will even give you which exit # to head for when you get off the train. You can purchase a transit card that will cover all your transit in the city.
For our family, we had diverse interests. We did an anime/manga tour one day. One kid brought an entire second suitcase for Pokemon items they brought back. I loved a family portrait session we did in kimono and samurai dress. This was in Asakusa and I did enjoy poking around the neighborhood there. We did a ramen food tour. We went to Yakatori Alley - it's next to Shinjuku train station and is a slice of old Japan. Admittedly touristy, but we had a lot of fun in one of the many tiny yakitori stalls trying new foods. DH and I lived in Japan 30 yrs ago, and had been to some of the main tourist check marks (castle, gardens, fish market) then, so we did not repeat them.
Teamlab gets a lot of traction on the TripAdvisor forum as far as recommendations. I do kind of wish we'd gone. It looks interesting.
I wouldn't recommend the Ghibli museum unless your family are Ghibli fans.
I find Kabuki super boring. (Sorry Miffy!)