It's also useful in that you can pre-order a Shinkansen ticket, for example, and link that purchase to your Suica card, which you then use for the Shinkansen gate. If there are other fees (which there may be) they're just deducted from the money the card holds, as usual. Makes everything very simple.
For me a physical card is easier than using a phone. A phone is so much larger so I would need to get it from a pocket somewhere, while the Suica card I can keep in my jeans pocket or some other easy place.