1. More dangerous world with over powered animals causing havoc on everything from weather to humanity... I mean, as we expand and destroy the environment animals now start moving into places searching for food.. Bears, baboons, racoons, all sorts of things.. What's stopping Pokemon from using their abilities, attacks, etc from stealing food and driving away humans, with no powers and just Pokeballs? If they were to exist. Your topic just said replacing animals, so Pokeballs potentially don't exist. Firearms could though I suppose.. But that would be... Bloody. I'll avoid that for now.

2. Zoophiles would have a ball, especially with ditto. >.>;

3. PETA (Or rather, PETP) would have a hell of a time trying to get people to go with another source of electricity besides Electric Pokemon, and other such things..

4. People would inevitably fall to their greed and use Pokemon for less than ethical purposes, and in far more realistic and harmful ways than Team Rocket. I'm pretty sure large flying Pokemon that can carry things hundreds of miles so quickly would be excellent for drug running, and Pokemon breathing fire, throwing electricity, blasting strong jets of water, causing explosions, magnetizing and causing electromagnetic waves and such can do far more damage than the firearms we have now.. If you put your mind to it, if you had the right Pokemon you could probably destroy and disable our current way of life with minimal effort.