For travelling with train (or any public transports in Japan) you can just use Google Maps and it's really Google Maps in steroid in Japan. You will know accurately in real-time all the trains and buses, and their respective arrival/departure times and even their rare occasional delays. All these real-time information are feasible because Japan contracted Hitachi company to provide the info trough the open API for other developers to access and it's very accurate. With Google Maps capabilities the integration with the real-time is just mind blowing to be experienced by any tourist, especially the Japan trains networks extreme timeliness.
I really wish someone come up with a VR or meta based game for tourist in Japan for buying souvenirs. This type of game was my favourite towards the end of 80s for shopping in London using the London Tube trains back in the Windows 2 time. It's only text based game and not real-time but it was an awesome gaming experiences nonetheless. Somehow I've forgotten the name of the game, but I think with all the 3D and real-time information available it will be a blast for the modern incarnation of the tourist souvenirs game to be based in Tokyo, or London.
https://boardgamegeek.com/boardgame/235344/tokyo-metro
But yes, 2D would probably be easier to navigate. 3D is more fun. Maybe that's the point, and the challenge of building it.
At personal levels, you either type in (time, origin, goal) into a map or a route finder app and get on trains in sequence as the app says, or do a rudimentary graph search in your head[2] and hope you don't hit 10 minute gaps between trains, which happens, but it's 10 minutes tops anyway.
1: https://www.gettyimages.com/detail/news-photo/corp-trains-il...
2: This shows hub and spoke model works for trains, but why not for air travel?
Trains are limited onto tracks and cannot merge out of the way, so point to point more quickly exhausts route capacity. Stations are less of a constraint.
Trains also lower the cost of transferring; airplane transferring is at best a hassle and at worst an ordeal. Meanwhile, trains can literally stop across the same platform across from each other so you walk a few meters at most. Japan does this a lot, where trains are timed to facilitate such quick connections.
[0] https://nagix.github.io/mini-tokyo/ [1] https://github.com/nagix/mini-tokyo
Probably an early prototype.