They are, but the fact of the matter is that trained Pokémon are far superior; or at least ones that are owned by highly skilled trainers. They're more powerful, and some will even know attacks that wild Pokémon can't normally learn because they can only be taught through the use of a Move Tutor, or Technical or Hidden Machines. There are also certain Pokémon that can't be found in the wilderness at all, and Team Rocket values rare Pokémon very much.