Please comment on our itinerary in Tokyo, we will be coming from Kyoto, a stop in Hakone for a night, and then arrive to Tokyo on Saturday evening. We are in our late 20s early 30s, and this is our honeymoon trip.

Saturday:
Arrive to Tokyo at around 6 PM , we’re staying at Shinjuku area, therefore planning to walk around Shinjuku for the night.

Sunday:
Morning – Ueno
Afternoon – Akihabara & Ginza
Evening – Shibuya

Monday:
Morning – Tsukishima Fish Market
Afternoon – Asakusa
Evening – Roppongi

Tuesday:
Morning – Harajuku
Afternoon to Evening – Odaiba

Wesnesday:
Leaving Tokyo in the morning.

You may want to spend Sunday afternoon in Harajuku for the coskids who are mostly there on the weekends.

I would group areas together.

Ueno, Ginza and Asakusa would be one morning/afternoon combo as they are stops on the Ginza line.

Per previous poster, I would go to Harajuku on the weekend if you want to see the cosplayers. From there, you can go to Meiji Shrine, Takashita Dori and Omotesando. Then I would do Shibuya at night from this area.

Also, Akabanebashi (Tokyo Tower) and Roppongi would be another grouping as they're two stops from each other on the Oedo line.

Rejigging Harajuku on Sunday and grouping things a bit together would look like this.

Sun:
Morning-Meiji shrine (I'd go earlish, like 8-9am when it's really tranquille).
Afternoon-Harajuku (Don't forget browsing through beautiful Omote Sando. Take a leisurely stroll to Shibuya)
Evening-Shibuya

Mon:
Early morning-Tsukiji fish market (the whole thing would be over by 9-10am)
morning/early pm-Ginza
Afternoon-Akihabara
Evening-Roppongi

Tue:
Morning-Ueno
Afternoon-Asakusa
(If you have time, I'd include Hamarikyu--the traditional Japanese garden along the bay).
Evening-Odaiba

I recommend you get a Suica card (there should be one that gives you better value combined with Narita Express) that would allow you to use both JR loop train around Tokyo and subways.

Thank you for all your response.

W9London, I read on the internet that I can only get the Suica card with Narita Express if I land at Narita Airport, however since I'm coming from the west, I don't think I have this option, is that correct?

No.....read this for information and a response to your questions

http://www.japan-guide.com/e/e2359_002.html

Aloha!