I usually buy direct in store. Shipping time zero. Prices have adjusted, at least around here, so that in-store prices aren't much different from the online ones.
Typically I'm browsing at a book store on the way home from work, and discover a book I might like. I could order it and get it a few days later, or walk out the store, book in hand. I'm an adult, with disposable income, so a hundred yen or two price difference doesn't matter to me. Being able to get the book right then does. Amazon is great for finding out what other people think about the book before I buy it.
Another example was my used oscilloscope. Buying second-hand things online is a gamble, and returning it is a major pain (get a cardboard box, arrange for the return and get and fill in a return label, be home to do the delivery). I went to a local shop instead. They hooked it up right in the shop to make sure it worked and to show me the basics of using it. And had there been a problem they would have come by in a car to pick it up directly. Much better. But Amazon did tell me which of the available models were better for me.