When you visit Tokyo you will have too many things to see, to eat, to experience, it will not be enough time to do all in a short stay.
This article will give you hints to think about how to go and see Tokyo especially for the first visit.
How long to stay in Tokyo - Overall picture of Tokyo
The period of stay I am recommending in Tokyo is 3 - 4 days. You will be able to visit most of famous places, it will make you satisfied.
But if you don't stay for such a long days, there are good ways to be satisfied even for 1 day or 2 days stay.
Map Source: File:Japan Tokyo Pref Map.svg
Generally speaking, it is mainly in the [23 wards of Tokyo] that tourists expect as "Tokyo".
The size of [Tokyo's 23 wards] is about 619 km².
Compared to other world big cities as examples, it is about twice as large as the central part of London. It is more than six times the area of Paris' 20th arrondissement (105 km²). Also, even compared to New York's Manhattan area (about 60 km²) .
You would see how huge the area is?
In Tokyo there is no clear distinction between the new town and the old town, new buildings and historic buildings are mixed in the same place. Depending on the location, there is more or less contrast.
In other words, there is no land concept applicable to 'Downtown' in America and 'Old Town' in Europe.
Many of the places and things to see in the 23 wards are packed within the range of the JR Yamanote Line（※） 1 hour lap train route. Within 23 wards, networks of trains and subways are stretched, and you can go anywhere using these transportation networks.
How about train and subway in Tokyo?
It is reasonable (cheaper) to visit famous areas by train and subway. However, it will be a little unsuitable for grasping the whole image of Tokyo when using trains.
Tokyo subway network is very busy and crowded especially on weekday. Transfer is complicated and it will take time to get used to. (When I started living in Tokyo for the first time, it took about 1 month to get used to train and subway network in Tokyo.）
In my opinion, when visiting a lot of places as much as possible in a very short period of time, these are not so very suitable. But I can recommend train and subway if travelers with less time restrictions, people who want to travel around on a low budget, or you clearly want to go to a specific place (Shibuya,Harajuku and so on)
Also, the peak hour of train and metro in the morning and evening commuter rush (08: 00-09: 00, 18: 00-20: 00) is crowded. You will be quite surprised at the sight of the crowded train.
It might be one of the most Japanese (likely) scenes and interesting experience, but is will be enough for you to experience just only once.
How to enjoy in 1-2 days (things to do)
If you visited Tokyo for the first time, I would recommend you to try "HATO bus tour" and "Sky Bus Tokyo（pop on pop off bus）". These allows you to visit the sights of central Tokyo more efficiently than trains. One of good points of these method is that you will catch the whole picture of a huge city of Tokyo in half a day or so. You will find the characteristics of a special big city.
Hato bus tour
Photo source :Hato bus tour
"Hato bus tour" is a pretty full-fledged short tour, as the bus operates according to a pre-determined program (itinerary) and the local guide accompanies it. "Hato bus tour" offer one of the most standard programs organized by a credible companies having been supported the sightseeing of Tokyo. You can check the general information and detail of Hato bus tour here.
Besides that, there is a program called "O Sola Mio" that you can enjoy Tokyo in a short time. This is a commentary on automatic speech in multiple languages, so you can listen to the commentary about the tour site with earphones. You can check the detail of the program here（O Sola Mio）.
It is an open-top two-storey bus tour, so if the season is good, it is very pleasant. The greatest merit of this is that we can see a wide range in a short time, so it is recommended.
Or there is Open-top Double-decker Bus Tours so if you do not have time, it's also recommended. The greatest merit of this is that you can see at a glance of a fairly wide range in a short time.
Sky Bus Tokyo（pop on and pop off bus）
Another is "Sky Bus Tokyo（pop on and pop off bus）". One of good points of these method is that you will catch the whole picture of Tokyo in half a day or so. You will find the characteristics of Tokyo.
It is more easy-going feeling than "Hato bus tour". You can get on and off as anywhere, anytime as you like in a certain period. You will be able to spend a lot of time at your favorite places.
The good things about this is that there are three courses that accurately covers the most popular places for foreigners in Tokyo. Especially "Asakusa, Tokyo Sky Tree course" and "Roppongi, Odaiba course" are popular.
Since the web site is automatic translation, it may be a bit difficult to use that point.
I introduce the image of sky bus from Jeff'sTravelGuide Tokyo video. This is not a pop on pop off bus, but the route is very common.
Source：Officila website of Sky Bus
How to enjoy in 3-4 days
If you have more time and opportunity, I would like to recommend using bus and train (subway) together. Or, I think that it is good to narrow down the places you want to visit and experience the place thoroughly. I would like to introduce the detail in another article.
If you have time to stay for about a week
Tokyo suburbs also comes into the choice. For example, Mr. Takao who is registered as a 3 star in the Michelin Guidebook of France and it has hot springs “Onsen”.
This place is popular especially among French people. Also, you can enjoy Hidden gems carefully in each famous place with the theme of “Deep Tokyo”.I would like to introduce this in another article.