Apple Maps Transit in Japan has a great transit data supplier, the same one as Google, but I don’t use it much. It’s just not that handy at finding the fastest route or cheapest route or route with the fewest transfer points, it doesn’t let me sort results or search for different train times on the fly.
For a map app the geosynchronous functions of Apple Map Transit are curiously weak. Even after engaging a route Apple Maps Transit has trouble keeping track of where it is or letting you know. Forget about geo anything if you are riding the subway, you’ll be in the dark the whole way.
Apple Maps Transit is a plodding one trick pony. That’s why everybody in Japan uses dedicated transit apps like Yahoo Japan Transit or the venerable Eki-supato (cleverly combining station-eki + expert = eki-supato, get it?). Not only do these dedicated apps find great transit routes quickly they let you sort results quickly by fare, fast, number of transit points, etc., or just quickly move to earlier~later blocks of departure times.
After you engage a route you have all kinds of granular alerts for transit points and destination points, and great geosynchronous feedback, you are here and your station is coming up. Eki-supato really knows their user base though, I mean a transit app really isn’t a Japanese transit app without “Drunk Mode” to make sure hard-working, hard-drinking salarymen don’t miss the last train home.