One tiny thing they could do to improve metro stations: Put big stickers on the floor that guide you to an interchange or an exit. Most stuff in Tokyo is "up" (overhead signs), but they could also use "down" to improve things. I was recently traveling on the metro in Kunming (Yunan Province, China), and I noticed they use the "down" part very well to guide you -- with Chinese and English. It was very helpful in more complex stations.

One more idea: Tokyo metro stations don't make a lot of use of colour schemes. I have used some metros that use very loud colour schemes all throughout the station to guide you to interchanges. Again: Very helpful for visitors.