When I visited Tokyo for the first time I quickly felt that the people of Tokyo were different than those in Fuji, a city whose tallest building was a 13 story apartment complex and being behind 3 people in a line for anything was a busy day. They are in much more of a hurry and more pushy than what I was used to. Tokyo truly does have a reputation for being slightly ruder than much of the rest of Japan.
However, it's important to put into perspective that rude for Japan is still infinitely more kind and polite than anywhere else. Take my last night in Tokyo as an example. While out for yakisoba in Shinjuku, I got to chatting with the cook, he was the only employee in the small restaurant (pictured below) that only had counter space for 6. We spoke about the fried noodle dish, a speciality from the area I used to live, what makes Tokyo an expensive city and cultural differences between Korea and Japan. After I finished my meal, I thanked him for delicious fried noodles and I asked him if he had any recommendations for a bar in the area. After asking me what my preferences are, none, he knew the right place to take me. He proceeded to walk me to his favorite whiskey bar, leaving the restaurant unattended, with 4 customers still inside, two blocks around the way. This sort of friendly, out-of-the-way kindness is far from uncommon anywhere in Japan. Friends of mine just got back from a trip to Osaka and had nearly identical stories to tell.