18 day itinery with 1,5yr toddler

Me and my wife are planning our trip to Japan this upcoming November, with our 1.5yr old son. We are very excited, so much to see and to do!
Without our son we would explore as much as possible but obviously we need to take in to account his pace (jet lag, mid day nap time, easy hikes, shorter travels) etc.

We expect that a travelling time between places of 2-3 hours per travel is ideal. Preferrably not more than 3 hours travelling.
Longer travels will be a bit more complicated with more transits, our luggage incl strawler, his need for food/drinks, opportunity for him to walk/play and rest/sleep.

We are considering 4-5 places to stay for a few nights so we gave enough time to explore Japan's life, culture, history and nature

Some places we really would like to visit:
Tokyo: around 4 days (sumo distric, fish market, uneo area/national museum/park, skytree, shibuya, akihabara etc)
Nikko: 2 nights (temples, hike/waterfall etc)
Kyoto: 4-6 days (garden, temples, historical area, geisha, tori gate hike, aquarium, incl side trips to Himeji and Nara)
Hakone: 2-3 days (onsen for us parents, lake/cable/rope/hike/
volcano)

(We have no real ambition to visit Hiroshima-area.)

... any additonal suggestions/ideas? for 1 more stay-over for 2-3 days?
We are looking for a place with nature/mountains/volcanoe/coast that's easily accessable. That would be ideal, where we can enjoy slow pace of Japan's outdoor life and hike+relax.

I looked in to Takayama/Kanazawa, but that might be a bit far. Or is it really worth it?
Same for Mount Koya. It sounds beautiful, but not so easy access from Kyoto/Nara with a toddler. And temple lodging, with fixes eating times and meals etc, sounds great but might not be ideal/flexible enough for our boy.
Maybe with all the temples in Nikko and Kyoto we have no extra need for even more temples in Koya...? or is it really worth it? hard questions no answer, i'm sure.
Izu Peninsula? Nagano/Alps?

So, would anyone know/recommend another rural+nature area, that is nice to visit, with easy access by public transportation between Tokyo - Kyoto?
Where we can enjoy rural/outdoor life in Japan, where we can hike a bit, relax a bit, stay in a low-key but nice traditonal lodging for example?

looking forward to hear your ideas!
Thanks!

Your plan looks easy paced and is fair to each location. You get to see enough to get more than just a feel of the place.

Kanazawa and Takayama is really nice. With the limited express trains from/to Kyoto and Shinkansen to/from Tokyo it is very accessible. These fast trains are more convenient and user friendly than others as the seats are wider, there are luggage areas, and toilets. There is a large garden and temple compound + historical districts in Kanazawa that is ideal for slow walks. The museums are also nice to feel the local culture.

Mt Koya is worth an overnight trip. No more. It is more for inner peace. The lanes and roads with very tall pines is really peaceful. The cemetery area and the temples are also very peaceful. You eat vegetarian meals and wake to the monk's soft chanting. However, everything is near (walk-able) even without considering that there are buses. You would take no more than 3 hours to see them all. So an overnight stay is all that is needed not 2-3 days. (Also it is very expensive to stay for a few nights)
Note that the eating times is not really fixed but you only after 1-2 hours period to request for it to be served.

Koya is for the experience in staying overnight at a temple. Living a life away from the secular world. And being filled with the mysticism of the area. If the cemetery mist over in the morning as the sun beams in, it is real serene.

Izu Peninsular is nice. Though with your travel pace, 2-3 days wouldn't be enough.

Nagano and Alps is possible, though if you find Kanazawa to be not a good transit point between Kyoto and Tokyo why go to Nagano? The water (onsen, drinking, and for cooking) is really nice. Also the trees are dense. If you like some nature walks, seeing wildlife and the like this would be ideal. Some fresher air is great for the young.

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For rural / nature / etc, Izu Peninsular and Nagano fits the bill. Kanazawa and Takayama are considerably rural and are small towns than cities but there is not much in terms of nature.

I would go to Toyama and Kanazawa. Both are cities by the sea. The former has nice views of mountains. Whereas the latter has Noto Peninsular Wagyu Beef (Yummy!). Both have good access to Sashimi and Sushi.

Oops. Didnt see low key lodging.
Usually that would mean a ryokan with an onsen.

Kaga onsen is near Kanazawa.
Ryujin onsen in Izu Peninsular is really hard to get to (need car) but if you want rural...
If not trekking the Kumano-kodo and staying in a bayside hotel are like Kii-katsura is ideal. Though time is against you here.

You probably don't wanna hear this. I'd be wary of spending big dollars on an onsen hotel and not using the facilities properly due to the toddler not being able to use them also.

Most/all onsens don't child still in nappies to enter the baths. If you and hubby can go solo why the other babysits, then it might work for you.