It seems like little by little the people with power to change things are starting to realize that one of the greatest problems that travellers find when they arrive to Japan is how closed and inaccessible the Wi-Fi and 3G ecosystem is (controlled by a few operators that make it very difficult to give you access if you are not a Japan resident). If you live here and pay your contract with one of the operators the experience is wonderful as you have 3G/LTE almost everywhere, but if you are a tourist Internet connectivity is a big issue.
However, from now on if you are coming to Japan as a tourist you will have free Wi-Fi in any NTT hotspot (FLETS) just by showing your passport when you arrive at the airport: here you have the exact spots where they will give you the required access information.
I think that right now this is the fastest, easiest and cheapest way to be connected in Japan during your travel. If you are going to be here more than 14 days 7spot and Frespot are other free options.