As copy-pasted from my note to krissehpoo, will have to edit when I have more time uvu
Set in a more modern Pokemon world, in which Pokemon got the ability to transform into humans/gijinkas whenever they wish (still need to make out more details on why). Most of them live their lifes pretty nicely, it's known that Pokemon usually have a nice relationship/coexistence with humans even in wildlife, so they're pretty happy to get their own job, house, friends, etc and they're generally peaceful with humans.
However, there are some that, now that with a human body they have access to abilities/tasks impossible before, believe themselves superior to humans and deem them unfit/unworthy of being the "dominant" race, especially because of all what they put nature through.
So, it's duty of some select people to stop them. These people have a "soul" Pokemon/s they're able to get the powers from, and basically go magical boy/girl style xD They're usually Pokemon Rangers and elite trainers not only because of their trust in bonds with Pokemon, but also because they have experience in fighting, taking on missions, etc.
Pokemon Trainers have strong transformations/powers, but only with their team Pokemon; Rangers have equally strong powers but only with their partner Pokemon, however, they're able to use powers, even if weaker, of any wild Pokemon they manage to befriend.
To clarify, humans are still the dominant race! Since they still have help of their faithful Pokemon, and technology as well. Most Pokemon who used to live in the wilderness though and are now gijinkas, even if don't agree with rebel Pokemon still prefer to be neutral than helping humans.
Also, Pokemon hybrids are allowed! They're usually born because of:
1- humans experimenting to have stronger allies against rebels
2- rebels attempting to do the soul thing between themselves
3- simply result of "breeding" between Pokemon gijinkas (although it's rare)
4- rare higher-ranked Pokemon (like Arceus' guards)