Recommendation for fourth trip

Hi everyone! We're going to Japan for 9 days in early april, this will be our fourth visit. We will spend 5 days in Tokyo basis, going on side trips to Yokohama and Enoshima, then 3 days Matsumoto, Nagano.
Our plan are these so far: in the first day we would do some hanami, and we're planning to go to Ghibli Museum and to the Mori Buliding Digital Art Museum.
My main question would be, what would you suggest, what to do, where to go, which are the hidden gems of Tokyo/Japan? We don't want to do popular tourists things anymore, as we've already done most of them probably. So we would like to feel and experience Japan in a deeper way.
I would be very happy if we could get any recommendation for the trip! :)

Thank you in advance!

Just some random ideas. You don�ft say what you like...

- walking through Sasazuka (or if a bit more touristy is fine : through Shimokitazawa, or maybe Kichijoji)
- cycling in Tokyo
- cruise boat from Hamarikyu garden to either odaiba or Asakusa
- walking over rainbow bridge (best from odaiba to Tokyo)
- visiting a sento

A bit outside of Tokyo:
- Chichibu

For sure there are million of other ideas. Have a look if any Matsuri is on when you are around.

Enjoy your trip to Japan !

There are over 3 dozen good places for day trips in the Kanto area - I sorely doubt you have seen them all. A few places include Nikko, Hakone, the Fuji 5 Lakes area, Karuizawa, Kusatsu, Izu, Kamamura/Enoshima, Kawagoe, Takao, Okutama, Yokohama, the Ushiku Great Buddha, Chichibu, Nokogiriyama, the Tanzawa-Oyama area, Minakami, Shosenkyo Gorge, Showa Kinen Park, and more. There are regional rail passes you can get for nearly all of them. A Tokyo Wide Pass might save you a fortune.
If you're willing to open your wallet a bit more, even more places are available - Sendai is just 90 minutes away by bullet train, and if you get a Nagano Niigata Area Pass, you can see a lot more places economically.
Same story for Nagano City - just 90 minutes or so away.
Even within Tokyo itself, there is still a lot. Probably you've seen some good city views from the Skytree, TMG, etc, but there are many more that few know about and are free.
http://supermerlion.com/10-free-tokyo-city-views/
There are a dozen traditional gardens to see also - maybe you've seen a couple, but there are some other exceptional ones that few tourists ever make it over to - Rikugien, Kyu-Shiba Rikyu, Kiyosumi, Koishikawa Korakuen, etc.
https://goo.gl/tAECfM

And speaking of which, almost certainly you've already seen Sensoji, but very few people go to see the "secret" Denboin garden next to Sensoji - and it's open just 2 months out of the year - your timing is in fact perfect.
https://goo.gl/q5nDom
Similar story for Meiji Shrine - few people ever discover Meiji Gyoen right in front of them as they blow past to see the shrine. Very beautiful and relaxing.
https://goo.gl/MgqXu5

There is way more to fill up several more visits.