Last time I was there Google Maps weren't good at navigating through the stations. And the signs at the stations were difficult to follow compared to other metro systems I'm used to.
I'm sure everyone is able to figure it out, but IMO they could take some inspiration from e.g. London or Paris.
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.
I'm sure everyone is able to figure it out, but IMO they could take some inspiration from e.g. London or Paris.