Then, about 2 gyms down, you meet a shady guy who wanted to be an artist but got rejected. He could be called "PkMn Trainer Adolph". He could eventually turn out to be quite a public speaker and get into pokemon-politics. Then, after gaining much power, he invades Poland. He soon decrees that anyone from Hoenn is an abomination, and the 'pure' nation must prevail over all others. He, and leaders from other Poke-countries get together and begin fighting a war in the Gen-5 nation. Soon, a group of People get together and bomb Kanto in an in-game cutscene called "Pokemon Diamond and Pearl Harbor". Kanto unwillingly joins the alliance of nations (conveniently called the "Allies), and begins to fight the war. PkMn trainer Adolph soon gathers up a large amount of PkMn Trainer Jews and puts them in Safari Zones, where they are forced to work in inhumane conditions. Eventually, PkMn trainer Adolph comes up with a "Final Solution"... he summons a legendary pokemon to battle all of the PkMn Trainer Jews and kill them. You, as one PkMn Trainer Jew, must battle/capture the legendary and allow the Allies to stop PkMn Trainer - Adolph, who later Gets Away Safely! from battle and commits suicide.
After the war is over, Kanto and Jhoto begin a Pokemon Race, starting an Ice-type Cold War during which they compete to see who can get the best pokemon. They use underdeveloped nations such as Orre and Fiore, which no one cared about before the War.
After all this, a couple of Poke-Extremists from Fiorre hijack a Dark Lugia and send it crashing into the GTS, igniting a sudden rise in racial profiling against Fiorre-ians, another game no one cared about untill Gen. 5.
All this being said, I think a war would be a great novel plotline for pokemon games. Too bad it's never gonna happen.