autumn season both hakone n nikko is worth a stay but personally i prefer hakone. but end of nov not sure still got autumn leave or not might wan 2 check tht

undertypo JR pass is not worth it at all if you are only staying tokyo area. for tsukiji, if you want to attend auction then must be there by 3am. if want to browse the inner market it only opens to outsiders at 10am. breakfast places open at 6am-ish? but the two popular places ppl will start queueing by 5am+.

I thought you went tokyo few times on work trip liao? Then shouldn't you know these things better than tourists? lol. If just tokyo area and if you willing to plan properly then the x-day metro passes can save a bit of money. But for me I don't bother, I just either buy single tickets or use suica/pasmo.

If you traveling out of tokyo like to kansai, nagano, etc then one of the various JR passes could be worth it.

JR pass not recommended to be used within tokyo
just use suica card

shinjuku is a good places to stay, many things to see around

end of nov in hakone will be cold, so expect it
worth a night stay if u booked a place with onsen which will be expensive
else just do a day trip

As most of them mentioned, don't use a JR Pass. Just get the SUICA/ PASMO IC cards for convenience of travelling from one place to another. The card can also be used like a Touch N Go. You can buy food from konbini such as Family Mart, 7-11 etc and pay with your SUICA/ PASMO.

Basically SUICA is issued by JR and PASMO is by Tokyo Metro, both can access each other's line and almost all the major rail stations/ network in Tokyo. You can get any of the card at the station and a deposit of 500yen is required when you get the card. Once you have it, all you need to do throughout the trip is just to top up the card when the credit runs low (top up available in all the stations via machine). When you return the card (in airport), you'll get your 500yen refund.

You may want to check this out too:
https://www.japan-rail-pass.com/common-ques...or-a-suica-card
http://www.pasmo.co.jp/en/

Hahahaha your list have covered most of the major attractions. Since you're there for autumn viewing, I will recommend the Shinjuku Gyoen 新宿御苑 (entrance fee 200yen for adult). Worth a visit for autumn foliage. But towards end November was just like the time I went last year, and autumn was coming to an end that time. So manage your expectation; there'll still be beautiful leaves here and there but a lot had fallen off by then. 

Other places you can consider going:

- Nakano Broadway: For shopping and anime enthusiasts
- Akihabara: Worth dropping by for a visit
- Yoyogi Park: Its just next to Meiji Shrine; you can pack lunches and picnic at the park. I find it a very pleasant experience
- Tokyo Station: Souvenirs, shopping, food - go down to Basement
- Odaiba: New Gundam is almost up, hopefully in time for your time - but also go there for breath taking night view at the Decks
- Ginza: Get to Chuo Dori on a weekend morning, around 11am and enjoy the car-less road at Chuo Dori, as its closed for pedestrians - landmark: Uniqlo
- Mt Takao: If you like nature - its a vVery pleasant hike with beautiful views and chairlifts/ cable car to ride, much to see as well. Info: http://www.japan-guide.com/e/e3029.html

Have not stayed in Hakone or Nikko, but it is very nice to stay in a ryokan. So choose one (be it Hakone or Nikko) and splurge for the night