if we take into account of Black Butterfree's post, that there will be 14 regions available, you could easily make a very interesting story, and a long lasting game
There is an interesting JRPG, but I forgot that name of it
you start off as the son of a king who ruthlessly killed the previous king, and threw the world into a turmoil of war (or something close to that)
the interesting part is the thing driving you (which I dont remember exactly, but I think you were trying to kill the king - like you get farther and farther into his castle, but you die or something)
anyway, you have descendants, and each one continues the story in a different region
what you could do, is have an evil mastermind controlling different pokemon, or a certain one, or a certain kind, or w/e
and have it be you travel through 2 regions per character, then you have a descendant, and continue through the next 2, and go on until you have traveled through all 14, then you have your last child who defeats the king, and then travels through any of the regions afterwards