Dear All,
Thank you for the advice. I revise my plan ,please comment or advise pn it. Thank you in advance.

27.11.18 (Tues, Kyota): Reach Osaka early morning. Take JR Haruka express train to Kyoto (80min direct).

28.11.18 (Wed, Kyoto): Cycling around Arashiyama Bamboo Forest (4 hours),Okochi-Sanso Villa,Golden Pavilion,.Stroll along Pontacho Alley.

29.11.18 (Thurs, Kyoto): Botanical Garden, Gion, Kiyomizu-dera and Philosopher’s Walk. Visit Nishi Market

30.11.18 (Fri, Kyoto): Day trip to Nara .Night bus/train to Kanazawa

1.12, 18(Sat, Kanazawa): Kenrokuen Garden, Kanazawa Castle

2.12.18 (Sun, Kanazawa) Visit Shirakawa go for few hours(Ogimachi Village for scenic viewpoint)

3.12.18(Mon, Takayama):

4.12.18(Tues, Matsumoto) ): visit Masumoto Castle , Daio Wasabi Farmin Azumino

5.12.18(Wed, Magome):

6.12.18 (Thurs, Tsumago):

7.12.18 (Fri, Hakone)nsen

8.12.18 (Sat, Tokyo): Harajuku (Takeshita Dori, Meiji Jingu), Shibuya(Yoyogi Park, Icho Namiki), Shinjuku (Tokyo
Metro Govt Bldg)

9.12.18(Sun,Tokyo) :Tsukiji Outer Market, Imperial Palace & Ueno Parkand Asakusa (Nakamise Dori) if timepermits.
Sorry, I have more doubts:
or
1. Should I spent 2 nights in Magome/Tsumago instead of 1 night each place?
2. Should I let go Hakone as the city mainly attraction is onsen and I can experience onsen in other places that I 'm going to visit?
3. Is there any places I should add in or let go?

You are going to be late for fall colors all around (probably). It would be a good idea to just spending the night in Shirakawago before continuing on to Takayama by bus. Have you considered Kamikochi and the area between Takayama and Matsumoto? If you don't go that way, by bus, then you might want to move Matsumoto after your Nakasendo hike.
1) Neither. You could take one of those two nights and add it to Takayama.
2) No. There is more to Hakone than onsen. It has some nature to love.
3) You could let go of any one or more of the destinations that you have between Kyoto and Tokyo because all of your stops are short.

Thank you mrwunfl for your swift reply.

Hi mrwunrfl,

Kamikochi is closed in December. What do you think if I omit Takayama and stay in Shirakawago. Does it make sense ?

Yes, it does. You will have more time for Kanazawa that way and the overnight in S-go is worthwhile. I think the road from Kanazawa to S-go is open year round (otherwise you train to Takaoka and then bus). Consider the possibility that some S-go lodging options could be closed on a Monday. The gassho zukuri where I stayed (Koemon) had snow boots available for guests. You can leave luggage at Kanazawa station or your lodging and then take just what you need for the overnight.

Thank you Mrwunrfl for your help. I revised my itinerary again. Sorry for that as I want to make sure I'm not overplanned . There are some changes that I made:
1. I decided to omit Hakone and go for Kawaguchiko as it is closer to Mt. Fuji and changes of seeing Mt. Fuji might be higher.
2. I’m not visit Matsumoto as it is just another city and I don't to rush from one place to another.
Below is my tentatively plan. Please enlighten us again.....
27.11.18 (Tues, Kyota): Reach Osaka early morning. Take JR Haruka express train to Kyoto
(80min direct).
28.11.18 (Wed, Kyoto): Cycling around Arashiyama Bamboo Forest (4 hours),Okochi-Sanso
Villa,Golden Pavilion,.Stroll along Pontacho Alley.
29.11.18 (Thurs, Kyoto): Botanical Garden, Gion, Kiyomizu-dera and Philosopher’s Walk. Visit
Nishi Market
*30.11.18 (Fri, Kyoto): Day trip to Nara .Night bus/train to Kanazawa
1.12, 18(Sat, Kanazawa): reach early visit Omicho Market, Kenrokuen Garden, Kanazawa Castle
2.12.18 (Sun,Kanazawa) :
*3.12.18(Mon, Shirakawago):Visit the villages , (Ogimachi Village for scenic viewpoint)
*4.12.18(Tues,Hirayu ): Hirayu Onsen
5.12.18(Wed, Tsumago ): Magame-Tsumago hike
*6.12.18 (Thurs, Kawaguchiko: Five lakes for viewing Mt. Fuji
7.12.18 (Fri, Tokyo ) :
8.12.18 (Sat, Tokyo): Harajuku (Takeshita Dori, Meiji Jingu Gyoen), Shibuya(Yoyogi Park, Icho Namiki), Shinjuku (TokyoMetro Govt Bldg)
9.12.18(Sun,Tokyo) :Tsukiji Outer Market, Imperial Palace & Ueno Park and Asakusa
(Nakamise Dori) if time permits.
10.12.18: Home sweet home
P/S We travel mainly by public transport. Sorry questions again…
1. Should I omit Nara (I’m not very keen in deer or shrine)? Any places that can fill in on 30 Dec?
2. Any day trip from Tokyo that I should not miss as a nature lover?

Where would you stay on the 3rd?
Hirayu Onsen does not really fit with the rest of your itinerary. That is, it would take more time/effort to get there and away. There is an onsen town or two just south of Kanazawa that would be on the way to Kiso Valley, or Hakone. Kawaguchiko? Ok, that will be a bit more travel than Hakone could be. One route to K-ko would be via Nagoya and then through or around Hakone. The other route would be via Matsumoto and then Shinjuku. On that route then it would be a good idea to stop in Matsumoto to visit the castle.

Well, Nara is much more than just deer and a shrine. And for what it's worth, you seem to be treating shrines as equivalent to temples (and they are not) and neglecting the fact that many temples and shrines are known particularly for their gardens. But you don't have much time in the area, so considering whether the time it would take to get from Kyoto to Nara makes sense.

Perhaps Nikko, Lake Chuzenji, and Kegon-no-Taki.

The main reason to go to Nara is to see Todaiji. It is more than a temple. It is historic and a great work of architecture. You can admire it for what it is but also for the fact that so many people have been involved in building it and maintaining for centuries. It has meaning beyond being a place of worship.
https://www.japan-guide.com/e/e4100.html
But, maybe you don't have time for it even if you are interested in it.

I wil stay in Skirakawago village(haven't booked). Due to time constraint, I think I will go Kawaguchiko or Hakone for onsen as well as scenic view. If you were me, which one will you choose?

Thank you kja for your advice. I read about Nikko, indeed it is scenic and worth going. But I found out that it is cold and windy in December.

Dear All,
We change our plans again.
WeI discussed and found that there is nothing really interesting for us in Tokyo (concrete jungle),so we plan to overnight there a night or two. As Hirayu Onsen doesn't to our route, we omit it. We're thinking of Hankone or Kawaguchiko to hve our onsen experience
Below is our plan, any comments or suggestions are welcome.

27.11.18 (Tues, Kyota): Reach Osaka early morning. Take JR Haruka express train to Kyoto

(80min direct). Visit Kiyomizu-dera Temple and Gion in the evening.

28.11.18 (Wed, Kyoto): Cycling around Arashiyama Bamboo Forest (4 hours),Okochi-Sanso

Villa,Golden Pavilion,Stroll along Pontacho Alley.

29.11.18 (Thurs, Kyoto): Botanical Garden and Philosopher’s Walk. Visit Nishi Market.

*30.11.18 (Fri, Kyoto): Day trip to Nara .Night bus/train to Kanazawa?

1.12, 18(Sat, Kanazawa): reach early visit Omicho Market, Kenrokuen Garden, Kanazawa Castle

*2.12.18 (Sun,Kanazawa)

*3.12.18(Mon, Shirakawago): Visit the villages, (Ogimachi Village for scenic viewpoint)

*4.12.18(Tues,Matsumoto/Takayama/?): ?

5.12.18(Wed, Tsumago ): Magame-Tsumago hike

*6.12.18 (Thurs, Kawaguchiko): viewing Mt. Fuji and onsen

*7.12.18 (Fri, Tokyo): ?

8.12.18 (Sat, Tokyo): Imperial Palace & Ueno Park and Asakusa(Nakamise Dori) if time permits.

9.12.18(Sun,Tokyo) : Harajuku (Takeshita Dori, Jingu Gaien), Shibuya(Yoyogi Park, Icho Namiki), Shinjuku (TokyoMetro Govt Bldg)

10.12.18: Home sweet home

We have few doubts: 1. Should we overnight in Kyoto for 3 nights and spend more time in other places

2. The 2nd day in Kanazawa, which places that we should not miss?

3. On 4 December, is there any scenic place to stay besides Matsumoto?We read Takayama is similiar to Kanazawa( please correct me if I’m wrong)

4. Where to do outside Tokyo for overnight/day trip for nature lovers?

Any comments and suggestion are appreciated.

First, while it is the modern heart and capital of the country, Tokyo is not all a "concrete jungle". Owing to its 400 year history, Tokyo has a huge number of beautiful traditional gardens and if you want to see nature, you'd be doing yourself a big disservice by missing them - Koishikawa Korakuen, Rikugien, Hama Rikyu, Kyu-Shiba Rikyu, Kiyosumi, Kyu-Yasuda, Meiji Gyoen, Tonogayato Gardens, Happo-en, Denboin in spring, and many more. There is also Takao and Okutama. Many places in Tokyo have some excellent autumn colors. Ginkgo Avenue at the start of December is breathtaking.
For other places in Kanazawa, the other big areas aside from Kenrokuen are the preserved old districts (chaya). You can still get a taste of Japan from centuries ago.
For day trips from Tokyo, many are in higher elevations like Nikko, the Fuji 5 Lakes or the mountains like Takao, so the autumn leaf season will mostly be finished. One other place you could try though is Kamakura & Enoshima. There is a good regional pass you can use for the areas as well. If you want to do some nature hiking, there are some good Kamakura trails also. There are some good places you can also go - Karuizawa, Kusatsu, Izu, Kawagoe, Takao, Okutama, Yokohama, the Ushiku Great Buddha, Nokogiriyama, Shosenkyo, Showa Kinen Park, and more. There are regional rail passes you can get for nearly all of them. A Tokyo Wide Pass might be a godsend.

Hi Adastra2200, thank you for for your helpful response. You indeed englightened me about beautiful places such as Ginkgo Avene, Koishikawa Korrakuen, Rikugien , Showa Kinen Park etc. I'm consider visiting Shosenkyo,Takao or Okutama. Can we visit Shosenkyo as a day trip from Tokyo and how to go there by Public transport?

https://www.japan-guide.com/e/e6952....tion_get_there

You might consider trying japan-guide as a first resource for your questions.