As you are probably aware, every Pokemon game has been set in a bite-sized version of a real-life region in Japan. Of course, after 4 generations of Pokemon there aren't a whole lot of settings left. I've color-coded a map to show you what's been used so far, and have decided what I think is the most likely region in which you can expect the new game to take place.
Note that the Kyushu region, the blue one for RSE, was rotated 90 degrees counter-clockwise in the game.
I think when it comes down to remaining geographically interesting locations, the most likely candidate for the new game is a combination of two geographic regions. These are the Chugoku region, which is the part of the mainland of Japan between RSE's and GSC's regions, and the island/region of Shikoku south of it. The combination of these two regions would yeild a lot of geographic diversity, including mountains, volcanoes, temples, jungles, oceans, large modern and historic cities, planes, a plateau, and even a desert-like 30km stretch of dunes.
So if you were wondering where Pokemon was going to be next, I'd put your money on this.
