One thing I've seen in small cities (Sakurai?) and suburban areas (Nagaokakyo) in Kansai is bicycle parking structures (similar to car parking structures) next to train stations.

By the way, there's an outfit that offers bicycle tours of Tokyo.

http://www.eok.jp/travel/tours/bike-...-cycling-tour/

I haven't taken one of their tours myself, but it sounds like an intriguing option for my next trip.