Last season, teams only spent one leg in Panama before heading to Atlanta.
As I recall south India (which IIRC is the speculated locale) has been a little more difficult to fly out of than other parts of India with more numerous international connections. It would make sense to me for two legs to be filmed there (with a minimum pit stop) and that would allow the legs to be laid out in a way to get teams on flights to Japan.
The other thing about Japan is that the producers would want flights that are direct towards Osaka (again the speculated locale) so as to avoid the areas north and northeast of Tokyo which were heavily damaged by the earthwuake, tsunami, and nuclear disaster. That, presumably means the teams would likely be going to an international airport on the west coast of Japan.