I have an iPod Touch, and I love the interface of choosing stations, and that you can get the route information without being connected. There is a lot to love in this app.
However, as an app for transportation, you have to get the actual transportation info right.
The app is missing stations on lines it includes - for instance, Chuo line does not include Koenji Station.
It should also include all lines, not just Metro/JR. Another station I looked up was Shimokita, which is served by two different rail systems, but it was not included either - presumably because Odakyu and the other rail arent included.
Lastly, including lines that serve the airports, even though technically outside of Tokyo, would help lots of people who are getting this app because they are traveling to Tokyo.
As it is, this app looks and works great. However, there is so much missing information, I cant rely on it.
Trout about Tokyo Metro