I find most advice on tourism websites or YouTube travel channels to be overly generic and agreeable. This post is the opposite! The intent is to give some specific (but possibly non-applicable!) tips that you won't see through those channels. The advice below is specific and may not suit you: travel is different for everybody and your mileage may vary. That's the beauty of travel.
Know your train station exits!
Japanese train stations can be ridiculously big. Shinjuku Station has 35 platforms and 200+ exits. The exits can be hundreds of metres away and can take 10-15 minutes to walk between. Different exits can place you on completely different sides of the city: if you exit Shibuya Station via Hachiko exit, you’ll possibly see the world’s most impressive road crossing and towers covered in LED displays. If you leave Shibuya Station via Tamagawa exit, you’ll see a bus depot and wonder why Shibuya is so boring.
If you’re unsure which exit to use to get to your hotel, phone ahead and ask them. Even though their English probably isn’t great, they’ll know what you’re talking about.
If you’re meeting friends at a station, meet them at a specific exit. If a friend has told you they are waiting at “the exit to Shinjuku Station”, you might as well go home as you will never find them.
Cities will have multiple railway companies.
In most world cities, there will only be a single rail operator. RailCorp for Sydney, MTR Corp for Hong Kong, SMRT for Singapore, etc. In Japan, there are multiple rail operators per city: Shinjuku station has JR East, Odakyu, Keio, Toei Subway and Tokyo Metro! What makes this fun is that these companies share the same train station real estate so keep in mind you’re looking for a rail operator plus a platform. If you mindlessly follow signs “to metro” or “to trains”, you might be heading to the wrong rail operator. I recommend memorising the logos and stylings of the rail operators.
Tip: Make sure you’re looking at the right map!
If you’ve picked up a train network map from a hotel lobby or a tourist information booth, make sure you’re looking at right rail company’s map. You could be looking at a Tokyo Metro map instead of a JR map!
Japanese characters to learn for train stations: Shin (新) and Juku (宿).
English signage in Japan is quite good. However, the onboard LCD displays that display station/arrival information can be slow to rotate between English and Japanese. If you memorise the Japanese character for shin (新) and juku (宿), you’ll be able to recognise Shinjuku (新宿) and guess when you’re at Harajuku (原宿). And if you’re on a Shinkansen (新幹線), you’ll know if you’re at a station that starts with "shin": Shin-Osaka station (新大阪駅), Shin-Yokohama (新横浜).