Seeking advise for Tokyo, Nikko & Hakone trip

This is our first time to Japan. 2 of us (my mum 68yrs old & I) plan to travel during either 3rd week of Oct or end of Nov for autumn leaves for a week in Tokyo, Nikko & Hakone. Each place stay for 1 to 2 nights, Tokyo city - just arrival & departure with a very brief city tour only.
In term of route convenience & cost saving. Greatly appreciate if could get adv/comment on my plan as below:

Day1 ARRIVAL,CHECK-IN TO TOKYO
Estimate arrv 0740hr at Narita Airport
Depart from Singapore by MAS airline // JR (NEX Tokyo Direct Ticket) + Toei and Tokyo Metro One-Day Economy Pass (1500yen + 1000 yen)

Day2 TOKYO/NIKKO(2hr)
Travel to Nikko after breakfast / Visit Temple, Lake Chuzenji //All Nikko Pass – 4 days(4,400yen)

D3 NIKKO
waterfall, Senjugahama, Yumoto Onsen
D4 NIKKO/ HAKONE (2hr + 85mins)
Hakone Free Pass – 3 days + Romance Car (5,640yens + surcharge of 890 yen+890 yen (from Shinjuku one way))
D5 HAKONE

D6 HAKONE/ TOKYO (85 mins)
after breakfast to Tokyo for Tokyo city brief sightseeing//Tokyo Metro Open Ticket (600yen)
D7 Tokyo / depart early morning
ETD : 1030 hrs Depart to Airport By JR Sobu Line(1320yen)

My Question :
1. May I directly toward Nikko instead of overnight at Tokyo (don�ft need to carry luggage to Tokyo city & cost saving ? )
2. Upon arrival, if stay at Tokyo, which area is more convenient for me to travel to Nikko on the next morning ?
3. All Nikko pass, incl round trip from Tokyo but from which station ?
4. Nikko to Hakone – travel back from Nikko to Shinjuku & transfer to Hakone by using romance car plus Hakone Free pass . any other better way ?
5. Which area will you recommend for overnight in Tokyo for next day early departure ?
6. Transportation offer special rate to kids, any discount for senior people ?
7. Any other better way for my plan on the route & transportation cost ?
Thank you very much.

Megan

1.In view of the plan you come to Narita flights at night, I do not recommend you to choose to go directly to Niiko. Takes 2 hours by train from Tokyo to Nikko, to become the long journey of continuous from your country. On the first day of your journey, it is recommended that is stored in the hotel luggage, it is walking and Sky Tree, Asakusa, Ueno.

2.Given the starting point towards the Nikko the next day, it is recommended that the Asakusa, Ueno, Kita-Senju around, you will be staying.
In order to go to Nikko, there is the means to ride Express Spacia that are operated in Tobu Line of private railways, it is starting from Asakusa, to stop at Kita-Senju in the middle.

3.The departure station in Tokyo that the Pass is valid is the Asakusa Station.
http://www.tobu.co.jp/foreign/pass/all_pass.html

4.It is a bit complicated route. It is recommended that you take a way to return from Nikko to Kita-Senju aboard the Spacia, from there, via JR Joban Line, JR Yamanote Line, go to Shinjuku.
The limited express train to direct to Shinjuku from Nikko has also been operated, but has gained a very popular, in the fall you're going, the train is to reserve a seat in particular is difficult.

5.Narita Airport is located to the east of Tokyo. I think in the same way as the first day, and good to find your hotel located Asakusa, Ueno, Kinshicho, Ichikawa around.

6.The Hakone free pass and ALL NIKKO PASS, child fee is set. There is no fee for seniors.
http://www.hakonenavi.jp/english/freepass/index.html

7.Consumption tax rate has been changed in April, ALL NIKKO PASS is now 4,520 yen.
You can buy the Hakone Free Pass at Shinjuku Station. Round-trip fee of Hakone and Shinjuku will include it. However, you must pay separately Romance Car fee.

I rewrite about 6. There is no pricing for seniors for Pass of the above two. It becomes the adult rate.

- Tokyo Subway Route Map
http://www.tokyometro.jp/en/subwaymap/pdf/routemap_en.pdf

[Transportation from Nikko to Hakone (Re: Questions 3, 4, 7)]

Unless you use Shinkansen (of JR-East / of JR-Central), your journey by rail from Nikko City to Hakone Town seems to require about 4 to 5 hours.

With an All Nikko Pass, you should start a trip by Tobu at Asakusa Station and finish it at either Tokyo Skytree Station or Asakusa Station.
: From these two Tobu stations, no train runs through to Odakyu Odawara Line.

I suggest you choose a Marugoto Nikko Tobu Free Pass instead. With this pass, you can start and finish a trip by Tobu at Kita-senju Station. This pass can be valid for 4 consecutive days, and the price is 4520 yen for a roundtrip from Kita-senju during April - November.
http://www.japan-guide.com/e/e2358_002.html

Choosing this pass, you can take the following route.
{Part A: With a Marugoto Nikko Tobu Free Pass}
Tobu-nikko (07:41) --[Tobu: Section Rapid]-- (around 10:00) Kita-senju.
{Part B: With a subway ticket (240 yen per adult) and a Hakone Free Pass}
Kita-senju (C-18; around 10:20)
--[Tokyo Metro subway Chiyoda Line]--
(around 10:55; C-01) Yoyogi-uehara (around 11:00)
--[Odakyu: a train bound for Odawara or Fujisawa]--
(around 11:30) Machida (11:40)
--[Odakyu + Hakone Tozan Railway: Romancecar (additional 620 yen per adult)]--
(around 12:40) Hakone-Yumoto.
: In Kita-senju, your can exit Tobu through South Gate, purchase subway tickets, enter Tokyo Metro subway through the same gate, and go down to subway Chiyoda Line platform in the basement using escalators.
: In Yoyogi-uehara, Tokyo Metro subway Chiyoda Line and Odakyu Odawara Line are jointed.
: Paying 1340 or 1440 yen more per adult, you can leave Tobu-nikko about 1 hour later, take a Ltd. Exp. Kinu from Shimo-imaichi to Kita-senju and reach Hakone-Yumoto about half an hour later.

A major difference between an All Nikko Pass and a Marugoto Nikko Tobu Free Pass is that the former pass can cover Shimo-imaichi -- Kinugawa Onsen -- Shin-Fujiwara while the latter does not. You do not plan to visit Kinugawa area, so I suppose the latter pass is enough.

Regarding Romancecar, I suppose it is worth checking whether you can reserve your seats, pay for Ltd. Express charge on credit and print out your tickets through the website.
http://www.odakyu.jp/english/romancecar/e_romancecar/howto.html

I recommend you get Hakone Free Passes and Romancecar tickets soon after arriving from NRT to Tokyo, for example at a counter of a major tourist agency.

[Transportation in and around Tokyo (Re: Question 7)]

Toei and Tokyo Metro One-Day Economy Pass (1000 yen)

You can choose a 1-day Tokyo Subway Ticket, which will soon become available on the next Monday for 800 yen.
http://www.japan-guide.com/e/e2017.html

[Accommodation in Tokyo (Re: Questions 2, 5)]

In Kita-senju, you can make a transfer among
Tobu (Isesaki Line, partly nicknamed Tobu Skytree Line),
Tokyo Metro subway (Chiyoda Line (C-18) / Hibiya Line (H-21))
and JR (Joban Line).

The area around Ikebukuro Stations of JR and of Tokyo Metro subway (Y-09 / F-09 /M-25), which is accessible by Narita Express, sounds nice for you to stay.
Starting from Ikebukuro of JR, you can use JR Yamanote Line�fs outer loop to Nippori then JR Joban Line to Kita-Senju. In Nippori, you can switch to Keisei Main Line via one transfer gate and take a non-Skyliner train bound for NRT.
: JTB, Kinki Nippon Tourist and H. I. S. have branch offices near East Entrance of Ikebukuro Station of JR, which are open not only on weekdays but also in weekends.

Thank you very much for your such detail advise. One more question here, as we try to avoid climbing up long staircase, which area/sightseeing we should by pass ? ie. Nikko Temple.

Admission ticket of the temple and shrine in Nikko had been sold once, but no longer now. Worshipers will be able to purchase admission tickets in various places.
http://www.nikko-jp.org/english/entrance/index.html

My mum told me she suffer knee pain after went up by staircase recently. Do Hakone & Nikko's sightseeing area need to do a lot of staircase clim up ? Thank you.