It couldnt work. Sure it'd be super cool to start out with a starter, and go out on your adventure, but think of the destruction they could cause. Ursaring, Tyranitar, Gyrados, Garchomp. They'd just rampage all over causing havoc. And instead of a Team Rocket, or Team Galatic, it'd be the government using these Pokemon. If a person could conceivibly capture a legendary dog or bird, he could control large portions of the world just with that Pokemon, not to mention the rest of his team. The government wouldnt have that, they'd send teams to find and capture all the Legendary Pokemon, and once there set off, that's just more chaos for the world to deal with. Besides, the 3-D versions of Pokemon wouldnt be so dandy for all of them, I wouldnt want to come face to face with a Pinsir, Beedrill, Krictetune, etc.
Be interesting if the world was structed like in the Anime/Games, but as it is now, much too dangerous of a world to bring in more possible dangers (that certainly dont outweigh the positives IMO)