Make allowances for jet lag. We missed breakfast most days so next time we won't bother with a hotel and will try air BnB.
Try to plan studio Ghibli tickets beforehand, we were too late.
Yes yes to Nara, Kyoto, Akibara.
When you land arrange to pick up a WiFi box thing so you have internet.
The best days were sometimes the unplanned ones just walking around.
Hara juku is also good for shopping and restaurants and there is a big park nearby.
The 100 yen shops are amazing! I think called Daiso.
Try to stay near a station which also has a stop on the JR bullet train line. Think like Paddington or Victoria so you have access to quick trains out of town for day trip but also tubes for local visits.
Good walking shoes as you walk so much.
Check our Time Out Tokyo for any one off exhibitions. We saw a Pixar one in Rippongi Hills which was fun.
Museum.of innovation is incredible with the robot demonstrations. Near that museum is a place to try a family friendly onsen. Online reviews all say how it's very touristy but we were the only Europeans there and they have a nice food market inside too. I think it's called odiaba.
Have a great time, it's impossible not to!