One of the fundamental paradoxes I've found in Japan is the contrast between the justly-famous efficiency of their manufacturing operations (in particular, the Toyota Production System) and the stunning inefficiency of many of their service-oriented operations. Checking into a hotel can often take 10 minutes, and don't even get me started on reserving a seat on a train.
I don't have a good explanation for it. It is not that it is an effort to make for a very personal, high-touch experience; most of it seems to be filling out multiple forms, many with variants of the same information, or going into multiple screens on a computer system.
It just seems odd, and I am trying to come up with at least a path-dependent "just so" story that at least helps me make sense of the discrepancy.