Not necessarily. The publisher doesn't have to own the studio to produce the game their making. Sony produces the Ratchet & Clank games, but they don't own the developer, Insomniac, who are independent, Sony does own the IP though, so Insomniac can't do anything with Ratchet & Clank without Sony's approval.
Marvel Games has some level of input, but it's the publisher who's mostly in charge. Spider-Man PS4 for example, is owned outright by Sony, with Marvel simply licensing the character to them. Same with Ultimate Alliance 3. It's Marvel, but it's Marvel licensed to Nintendo. Or the Fox X-Men franchise in the case of film.
@bolded: That's the thing! Who owns the IP calls the shots. Nintendo owns nothing there, so they ain't in any position to call any shots.
@italic: that's only true for the movie rights. Marvel retained the rights for pretty much everything else. It's just that Sony also makes the Spiderman video games, and thus doesn't want to share with the others, but afaik they don't have any exclusivity rights over him outside of movies.
The Nintendo eShop rating Thread: http://gamrconnect.vgchartz.com/thread.php?id=237454
The Steam/GOG key gifting thread: https://gamrconnect.vgchartz.com/thread/242024/the-steamgog-key-gifting-thread/1/