Tokyo - Kyoto - Fuji/Hakone - Tokyo

Hi,
This is my itinery for cherry blossom viewing next year and I have a few enquiries. I will buy the JR rail pass for this trip.

1) land at Haneda at night On 6 apr 2018 (fri)
Question 1: I will be landing at Haneda airport at night, 2150, Are there any recommendations for hotels that are along the Haneda limousine bus routes at either Shinjuku or shibuya or ikkebukuro or even Ueno so that we can take a direct bus there after checking out of customs? Or is it pretty risky and it will be better to stay at the hotels near the airport instead and then head over to Tokyo to check in next morning?
I am travelling with wife, toddler and 2 parents so I am thinking traveling by bus might be easier as compared to train

2) (7 apr sat) explore Tokyo: Asakusa, Ueno, Tokyo sky tree night view (not sure whether to add in akihabara on this day or not)
3) (8 apr sun) chidorigafuchi, Shinjuku Gyoen, Meiji shrine, harajuku

4) (9 apr mon) use JR pass to travel to Kyoto
Explore Kyoto: Ginkakuji, philosopher path, heian shrine / imperial palace (undecided)
5) (10 apr tues) fushimi inari shrine, nijo castle, kinkakuji
6) (11 apr wed) Kiyomizudera temple, Maruyama park, yasaka temple
7) (12 apr thur) arashiyama and sagano

8) (13 apr fri) use JR pass to travel to Kawaguchiko, rent a car and self drive to shibazakura festival, visit northern shores and eastern shores of kawaguchiko to see more mt Fuji views. Stay at kawaguchiko.
9) (14 apr sat) drive to gotemba for shopping (optional) check in hotel at hakone (any recommendations?) in order to leave luggage, then return car before taking the hakone round course.
Question 2: any recommendations for car rental that allows renting at kawaguchiko station and returning at hakone machi or Moto or yumoto which will Allow me to start the hakone round course?


10) (15 apr sun) use JR pass to return to Tokyo for R&R
Question 3: what is the best way to maximize my JR pass for this trip?
11) (16 apr mon) tsukiji fish market and shibuya
12) (17 apr tues) departure from Narita

If there are any parts of the trip that is too rushed, undo-able, or needs revising, do let me know as well. Thank you! Appreciate it.

regarding to 3rd day : chidorigafuchi, Shinjuku Gyoen, Meiji shrine, harajuku
Chidorigafuchi, Shinjuku Gyoen and Meiji Shrine are very big places, you will get tired before going to Meiji Shrine.

Noted and thank you! I will revise the itinery for that day and probably push Meiji shrine to one of the last 2 days..I think there's not a lot of cherry blossoms views there compared to Shinjuku gyoen and Chidorigafuchi?

Do let me know regarding my first two questions as well if you are familiar with the areas. Thank you!

In regards your first question, check the information on this page
https://www.japan-guide.com/e/e2430.html

It maybe better to book a hotel near the airport given that public transport does not operate 24/7. Unless, you can afford a taxi to a hotel in Tokyo, and the hotel is ok with you arriving around midnight.

8) (13 apr fri) use JR pass to travel to Kawaguchiko, rent a car and self drive to shibazakura festival, visit northern shores and eastern shores of kawaguchiko to see more mt Fuji views. Stay at kawaguchiko.

Are you aware that it is like 5 hours journey from Kyoto to Kawaguchicko with about 4-5 transfers, some of them maybe in Tokyo?

If you're going for the shibazakura festival check the dates it will occur in. You maybe a bit early for it on 13th April
https://www.japan-guide.com/e/e6919.html

I'm just wondering why don't you go to Kawaguchiko from Tokyo, it's a shorter journey of about 2.5 hours by direct bus from Shinjuku?
https://www.japan-guide.com/e/e6906.html

I don't know about renting cars in this area so I can't provide advice on that, but there is a Fuji-Hakone pass that covers public transport in the area you want to visit, check more information on that on this site using the search button.

In regards your return flight, I'm just curious why is it from Narita and not Haneda like your incoming flight?
Anyway, if you want to leave the Mt Fuji five lakes/Hakone area to the end of your trip rather than Tokyo you can check direct access from there to Narita airport (hoping that you're flight is late in the evening and not in the early morning).

Cos you are not doing a full round trip between Tokyo and Kyoto. I don't think you need a JR 7day pass.

Your only big travels are Tokyo to Kyoto, Kyoto to Mishima, Odawara to Tokyo. You could put them into a program like hyperdia or similar to see if you come close or over 29,XXX yen.

Also from from the sights you wanna view in Kyoto, you'll be using more non JR services that JR services.

As for the car renting question. I'd probably pick it up and return in Odawara. Pick it up, drive to Gotemba etc and Fuji 5 Lakes, then back to Odawara are return it. Then do you Hakone sightseeing.