Pffft the beauty of the Pokemon world. Is that it is rife with chaos! Fine, let's toss out the intrusions of man, being what they are. If of course you're going the route of the cartoon, sans logic. -Forget that Ash totes about a Pikachu from Kanto into every region, or that transporters allow one to take a Pokemon from any region in their PC with them into battle.-
What abut the aliens? Yes, all the alien Pokemon -Deoxys and that stupid wishing star thing- Or all the time traveling, dimension warping, dream twisting, earth, fire, wind, air, water, ice, land, storm destroying legendary pks; that constantly put entire regions in jeopardy should they get so much as the sniffles! -or be summoned by some moron who 'does not know their power'-
Let us also remember all the endangered Pokemon..Hunted and captured into near non-existence. The ones that are usually bred up in a Pokemon Reserve, or Safari.
I see your point...So..Why not make a Pokemon reserve? That holds exotic/non region oriented/nearly extinct pokes. That people can go and..catch...in said reserve. Even if they're hard to catch!
Also..EEVEES! Eevees should be the new rats. They were free in the original game, and they're linear evolution cycle is broken. I demand an Eevee! Might as well be a rat with the way it's all brown. Dark beady little eyes. Rat in disguise I say!
OR..orrr.. Honchkrows! -and murkrows- Honchkrows are now in game. Let em loose I say, roam free and control all the little murkrows!