Well, there's a tiny discount of a few yen vs buying individual paper tickets. While the convenience far outstrips the tiny yen discount, it does make a difference towards the end of your trip as you're running out of physical yen, don't want to exchange more money, and are trying to draw down the card before you leave. Nearly all of the machines make you top off at 1000 yen intervals. That's a LOT. I found a couple that let me do it at 500 yen intervals and only one where it was, I believe, 5 yen intervals.

I came from Osaka, so I had an ICOCA card and couldn't return it for my deposit/remaining balance. You can only return for deposit in the home region of the card. In any case, the little tiny discounts added up and I was able to squeeze out my last 500 yen top off.

Oh, and I found Google Maps to just be a lot easier to use. It's far from perfect, and combined with the iPhone's (we had a 6+, 6S, 7, and X going at once at times) awful compass, be prepared to be frustrated and lost. Still, I found it a lot easier than Hyperdia. Even for planning, unless you know the exact minute you are leaving, I just found Google Maps easier. For most tourists, it's impossible to plan to the minute. Not when there can be a new train in a couple minutes that might change up the best option and you're slow in figuring out which direction to walk.