Hardcore fans may like the BVE train sim [1]. A lot of Japanese fan-made lines (add-ons) with custom sounds. Generally speaking, the game is far from AAA, but the "hand-made" feel makes up for that.
The downside is that sometimes it is difficult to install addons or to figure out their custom features because the instructions are often poorly translated from Japanese and websites often have no English translations at all. One should also note that some addons include and run "homemade" DLLs to implement custom features.
It seems that the community is on the decline though, because while searching around I have found a lot of dead links. One can try OpenBVE [2] (partially compatible with BVE), which is less Japan-centric but should have some Japanese lines.
Or the official JR East Train Simulator https://store.steampowered.com/app/2111630/JR_EAST_Train_Sim...
Though very pricey especially if you want the Yamanote line DLC too... https://store.steampowered.com/app/2514660/JR_EAST_Train_Sim...