Well like any transport system in Europe is complete trash, and you won't agree because you don't know any better until you come in japan. Helas, when you thought you were a silver sardine in Londen the sardine effect is a lot worse tho in Japan in comparison to London,Paris,Amsterdam it feels like a golden sardine compressor where you gasp for air, especially during summer its bad. Although the system is a lot more modern, using the subway in Tokyo during rush hour is well ehm just watch this.
Train to Ofuna from Shinagawa Tokyo - YouTube
However i feel very happy and would like JR to replace dutch NS immediately. Shinkansen is fantastic, i cry with tears every day so much more better and efficient Japan is.
But i really like the old fashionated London subway tho. If there's one thing England beats other countries its at feeling that you are home. Even tho i am from Holland, i never felt a feeling of belonging as i did in the heart of london.