I mean, is it really any more complicated than any other big city around the world?
The remarkable thing about the train system in Japan is just how connected everything is. Sure, you may need to change trains a few times, but you can practically travel anywhere you want by train (and a little walking).
I think you’ll get used to it. Once you get the hang of it, you’ll be using the trains without even thinking about it.
Here’s a video that does a great job teaching you about taking the train in Tokyo: