Itinerary & Best Transport options

Hi to all! I am trying to find the right options but is so much information, so many transport packages that is very hard to take the right decision and I need an expert eye.
Our Tour in November will include: arrival to Osaka Kansai Airport, 2 night Osaka, 3 nights Kyoto, 1 night Nagoya, 6 nights Tokyo, plane back home from Tokyo airport. We want to visit Nara, go with the bullet train, I would like to see Mt Fuji from afar (but without having to loose a day on the way, considering that we will be traveling with luggage). Do you suggest we should totally see as well other cities or places? What can we do 6 days in Tokyo? What passes should we buy?
On the first day we arrive in Kansai airport at 10AM and we have a hotel near Kintetsu Namba Line and we want to start visiting, considering that we only have 2 days and we wish to go to Nara as well. Should we buy a Yokoso Osaka ticket or should we buy a Icoca&Haruka and pay as we use. From Osaka to Kyoto/ Kyoto-Nagoya/ Nagoya - Tokyo: should we buy a pass or buy individual tickets? Thank you very much!

You can consider Japan Bus pass 7 Day=15000 yen cover Tokyo,Osaka Kyoto etc prefecture.In Tokyo,3 Day subway pass=1500 yen.Good Luck

With the open-jaw itinerary you have, the full JR Pass would not work for you. And without extensive travel in the Kansai area, the typical Kansai passes would be unlikely to pay off either. Though there is the Hankyu Tourist Pass that might work for you,
https://www.kansai360.net/m/en/ticket.html
but it also depends on where you are going.
https://goo.gl/K3RqXH

The Icoca & Haruka discount ticket is one way to save money on the Haruka train, and you can still use the Icoca card in Tokyo. I also don't see why you switch hotels with 2 nights for Osaka, and 3 nights for Kyoto. It's just 30 minutes by train between them. Plus if you are already seeing Tokyo, there is far less need to spend your daytime in Osaka. Nara is well worth your time though. If you have limited time, you can see most of the best at Nara Park in half a day.
https://youtu.be/6-Byqd2u8fM

Personally, I'd skip Nagoya entirely - if you want a place to stop off in between, you could see Kanazawa via the Hokuriku Region. You have a wide range of places you can see as day trips from Tokyo - Nikko, Hakone, the Fuji 5 Lakes area, Karuizawa, Kusatsu, Izu, Kamakura/Enoshima, Kawagoe, Takao, Okutama, Yokohama, the Ushiku Great Buddha, Nokogiriyama, Minakami, Showa Kinen Park, and more. With good weather, you could see Fuji from Izu or Tokyo, if you don't go closer to the mountain.

Haruka pass is probably a waste of time since your hotel isn't on a JR line. Just use hyperdia and travel on local and rapid trains to get to your hotel since it is on the southern side of Osaka. It will be a quick trip anyway.

And IC card would be good for both Osaka and Tokyo. And I'd probably get a one way ticket from Kansai/Osaka to Kanto/Tokyo.

Which passes to get would depend on where you choose to visit locally. Which you haven't mentioned. So cannot help on that question.

Can we buy online the shinkansen train tickets?
Kyoto to Nagoya on Nozomi train (aprox. 5170yeni per person)
Nagoya to Tokyo on Nozomi train (aprox. 10,560 yeni per person)
On the WestJr I saw the timetable and price tickets, but I don't see where I could buy it online. https://www.westjr.co.jp
I entered on the https://shinkansen-ticket.com and the tickets are at least 30 euros more expensive...
Thanks.