There's so many ways to discover Japan. You can get around by train, subways, buses, ferries, and air.
Train travel to me is the trickiest and most overwhelming part of planning since there's Japan Rail and local subways (owned by different companies).
There's a multitude of regional (discount) passes on offer and information changes all the time.
The New Chitose Airport (CTS) | CTS Airport Map
Haneda International Airport (HND) | HND Airport Map
Narita International Airport (NRT) | NRT Airport Map T1 | T2 | T3
Chubu Centrair International Airport (NGO) | NGO Airport Map
Kansai International Airport (KIX) | KIX Airport Map
Osaka (Itami) International Airport (ITM) | ITM Airport Map
Fukuoka Airport (FUK) | FUK Airport Map
Kagoshima Airport (KOJ) | KOJ Airport Map
Naha Okinawa Airport (OKA) | OKA Airport Map
Maybe it's just me, but I like to consult the airport maps to get an idea of where everything is located (ATMs, information counter, restrooms, bus ticket counters, train station, etc.).
Armed with information in-hand, I do a pre-walkthrough in my head prior to landing.
There's no need to worry about getting lost, transfers, or finding a seat.
It's also inexpensive too.
I talked more about it on it's own page.
- Compare to see if getting a JR rail pass is beneficial vs. pay as you go on re-loadable IC cards (SUICA/ PASMO/ ICOCA, etc.). You must purchase a JR pass voucher before arriving in Japan (~ 90 days prior to arriving).
Osaka Aquarium + 1 day Subway/ Train pass.
(KIX Airport --> Kyoto)