We returned from our first trip to Japan in mid-July and about the easiest time we had was navigating the trains. We used our JR rail pass for almost all of our travel.

Not sure where you got your information from, but every train we took - all information was in Japanese and English, whether spoken or on the information boards, platforms included. And if we had a question someone was always on hand to help.

There is plenty of room for luggage, but if you are worried, you can prebook luggage for the bullet train from Kyoto to Tokyo. However, we never did and never struggled to find space. However, I guess it depends on how much luggage you have.

On our last day, we travelled back from Mt. Fuji on The Romance Car and transferred to Haneda Express.

We never considered flying as taking the trains is a very memorable experience when visiting Japan.

I am sure there are others who can chime in with more precise information for you to make a decision.