In a recent recording with his colleagues, Game Freak director Junichi Masuda explained how he thinks everyone is under the impression that Nintendo is the developer of the Pokémon games. Masuda’s reference is a poll that asked 200 people about who they think the true developer is and all participants went with Nintendo as their answer. Masuda then went on to say how he and his team are aiming to change this impression by differentiating between the two entities.
Source: Game Freak