While Nintendo might have some say in what goes on with certain aspects of Pokemon games, they mainly act as the publisher. Development duties are handled by Game Freak, and have been since day one. Game Freak's Junichi Masuda wanted to make that clear in the latest episode of Game Freak's YouTube series.
Masuda talked to 200 different people to ask them who created the Pokemon games, and apparently nearly 100% of those people pegged Nintendo as the developer. Furthermore, those same people believed Masuda worked for Nintendo, and not Game Freak.
Moving forward, Masuda is hoping that more people come to learn that Game Freak is behind the Pokemon series.