How often you ended up in a train systems where you had to figure out 'Ok, so how much do I need to pay know?' and saw like the areas were divided into zones, sometimes even in separate charts.
In Japan I found it very easy, despite there are even completely other characters. The easiest thing is you look for a station and the price in Yen is well-placed within the whole map. And even if you get it wrong and pay not enough: Once you leave the train there are machines where you can fix your ticket with paying the remaining Yen - or just go to the counter on the way out. All you need to know is the station you wanna go to.
You cannot leave unpaid - the system is so simple and so effective working. No need to worried, did I pay enough? Recently I took a longer way from Mishima to Tokyo and then I in Tokyo I went out at the Ryogoku station. I only payed a small amount at the beginning for the train (like 230 Yen) and payed the rest at the final subway station - after changing the train three times during that ride. No issue at all (as it was all JR line).
And since there are often different lines - especially in big cities like Tokyo - there are so many ways to reach the destination you want to, and even in cheaper ways than you initially think.
That's something I noticed this year when I was going from Osaka to Suzuka: According to Google Maps I saw a certain price, but in reality it was around 1000 Yen cheaper - by only using certain trains - with a short stop in Nabari and Ise.
Additionally I should mention that you can use prepaid IC cards which allow you to travel faster and more convenient. You can also use the machine to check how much you paid for what and how much money is left on the card.
For longer routes you should consider getting a Japan Railpass, where you have a flatrate for certain lines around the country.
Does it make financially sense? Depending on the routes and distances you take sense - but don't forget to get the pass in advance.
In general (to sum up) you should go to Japan and experience it yourself!
