As an example, here is a picture of what I saw in Kyoto when I went to a higher-up restaurant:
Here is a picture from about the same height in Tokyo:
The visual differences between Tokyo and Kyoto reflect the different cultures that are found in the cities. Kyoto was very much about the preservation of the past and the quiet serenity that Japan is known for. This is reflected in the fact that the buildings there are relatively short, and, as I have stated in a previous blog post, the city does not encroach upon nature, but instead tries to work with it. Tokyo is about moving forward; it seems that builders were not concerned on what they were encroaching on, they just wanted to build as high and as fast as they could. Progress does not include building around what is there first, you just build through it. There is no serenity in Tokyo and very few visual nods to the past. You either go forward or go home.
Whether or not one city is better than the other is a matter of personal preference, but I will say that that they are most definitely different. It’s no wonder that tourists always want to go to both Tokyo and Kyoto; they are two vastly different places, but they are both Japan.
This is just one comparison of cities in Japan. For Osaka vs Kyoto, check out Mijoe's blog here.