in 15 days you have plenty of time to explore in those locations. For nature, spend more time in the Japanese Alps for hiking. Koyo (fall foliage) would be at peak above 1500m in mid-Oct.

check out one of my koyo visits crossing the Alpine route, Shin-hotaka and Kamikochi in mid-Oct 2010.

https://japantravelinsights.com/2010-the-alpine-route/

The annual Takayama Autumn Festival is held on 9-10th Oct.

https://www.japan-guide.com/e/e5909.html

>>Or should we leave Tokyo straightaway and do Tokyo at the end of the trip?

there is no right or wrong. either is fine. If your party needs to adjust jet lag consider staying in Tokyo for 2-3n right after arrival.

>>Also is it advisable to drive outside of Tokyo or is public transport with luggage transport taqubin better?

Indeed, driving in megacities in Japan is not recommended. Use efficient public transports incl in most rural areas except in Izu Peninsula. Due to infrequent public transports a car is recommended for at least 3 days.

Thank you so much!

I read that alpine route takes rather long more than 6 hours so I’m not sure it’s too long for the kids :(

If we skipped that and did Tokyo-matsumoto- kamikochi-takayama, is it better to break the trip from Tokyo-matsumoto with a stop in Kiso or karuizawa?

I understand there are two ways to get to Matsumoto- Azusa or Shinkansen, which is better? If it takes 4 hours it is rather long..

Also if we wanted to go to Fuji how would you recommend to slot it in?

Ideally hope to stay 2-3 nights per place so it’s less tiring with the young kids.

Places of interest: mori squirrel/ hiss limestone/hide no Dato village. We are ok to skip shirkawago and kanazawa if necessary.

Is it better to stay in hirayu or one of the hotels in kamikochi for easy access to walks ? Thanks so much any advice appreciated!

Tokyo/Shinjuku and Matsumoto are served by the JR Azusa express train in less than 3 hours direct. No Shinkansen train serves those 2 locations.

Matsumoto (3n) - base for day trips to Kiso valley, Nagano/Kids Ninja village etc.

https://www.japan-guide.com/e/e6007.html

Kamikochi - alight Alpico bus at Taisho-ike and walk to Kappa-bashi in 1 hour. Trails are flat so easy even for small kids. From Kappa-bashi onward to Meijin-ike and beyond trails are strewn with large boulders so unlikely suitable to them.

https://www.kamikochi.org/plan/trekking

Either stay in Kamikochi @1500m or Hirayu onsen @1200m. While there are hotels/ryokans in former it's relatively more expensive and easily get filled up during peak koyo season in Oct.

Takayama and Hirayu onsen are served by frequent Nohi express bus.

Fuji 5-lake - easy day trip from Tokyo by frequent highway buses from Shinjuku BUSTA in 2 hours. If viewing Mt Fuji is a main goal better stay 2n to increase the odds. It can be viewed only on clear days. From Kawaguchi-ko, take local route bus to Kofu in 1 hour and connect JR Azusa express train to Matsumoto in 1.5 hours direct.

Search for routes, fares.

https://japantravel.navitime.com/en/area/jp/route/

Thank you so much!l for your input.

From takayama, would it make sense to fly out of Japan from Nagoya? Or would returning to Tokyo be better?

I understand train is fast but it’s also expensive? And I’ll have to pay for the 2 kids with takubin if sitting on our laps would be quite uncomfortable?

Would driving throughout be better?

If an open-jaw air ticket works out for your party (itin and cost-wise) why not ?

Given the age of your kids they are free to travel on city subways, commuter trains and local buses. If they occupy a reserved seat on express train then child fare (at 50% of adult) applies.

https://www.japan-guide.com/e/e2460.html

By car, it makes sense in Fuji 5-lake area and in the Japanese Alps along your itin. Note that no private car is allowed into Kamikochi. All private cars have to be parked in 2 designated parking lots (with fees) and connect Alpico bus into K.

https://www.japan-guide.com/e/e6040.html

you may refer to one of my recent drives in last Aug visiting K and Takayama. Rental car was picked up in Matsumoto and returned in Nagano city with no drop-off charge.

https://japantravelinsights.com/jp-2023-aug-jp-alps-part-1/

@dli_hk thank you for your input, in that case, would it make any sense to drive through from Tokyo to fuji , Matsumoto, then to takayama and then to Nagoya ?

We have about 16 nights in Japan and hope to spend perhaps 5N to 6N in Tokyo.

How many nights do you reckon I need to explore squirrel forest, hida folk village/ limestone cave and also do some day hikes in kamikochi?

Is it possible to base in takayama and travel to kamikochi?

I saw hirayu seems unavailable for mid October, and kamikochi hotels are in the range of 700,000 yen a night.

would it be ok to base in takayama itself or in okuhida like Hakunnsou / Yumoto ?