Shigeru Miyamoto worked in a Producer/Director role in most of his key games up until Zelda: Ocarina of Time. Miyamoto was a director on Super Mario 64 and had a Producer/Director role on Ocarina of Time.
Sometime between the NES and SNES eras Miyamoto got in trouble for giving himself a "producer" title to the western press because they wouldn't understand the hierarchy of their Japanese development teams. (Meaning "Producer" and "Director" and "Section Chief" might mean something different)
http://web.archive.org/web/20030811223536/http://www.video-fenky.com/features/miyamoto.html
I: So why did you begin calling yourself a producer?
SM: Once we finished Mario and Zelda, the next thing I wanted to do was sequels. I thought Zelda could turn into a new and different game if the game system was more fun and we could switch between maps and things, so... I had people under me do Mario 3 and The Adventure of Link, so I figured, hey, I'm a producer now.
There's also one more reason. To tell the truth, in Nintendo there aren't any official positions called "director" or "producer". Instead you have the kacho/bucho (section chief/department chief) system. The thing is, though, people overseas don't get that system. So when I started dealing with overseas folks, I wanted to sell myself to them, so I just wrote "producer" on my business card. With that title, people from overseas could recognize what I do, and it worked all right. Later I got yelled at from the head office about assigning myself titles, but... (laughs) Those are the two reasons I started calling myself a producer.
[Takashi Tezuka worked directly with Miyamoto on Mario and Zelda, and Tezuka directed Super Mario Bros. 3, The Lost Levels (Miyamoto was 10% invovled), and Zelda: A Link to the Past. Kensuke Tanabe directed Doki Doki Panic and designed levels on SMB3 while Miyamoto was "Producer" with a director role]
http://www.nintendo.com/nes-classic/super-mari-bros-and-super-mario-bros-3-developer-interview
Miyamoto became directly involved in Twilight Princess towards the end with the young development team being unfocused and after Aonuma had to step in to direct.
http://iwataasks.nintendo.com/interviews/#/wii/twilight_princess/0/5
Aonuma I suppose that's true. In any case, it's a fact that if Miyamoto-san thinks of something, he wants to tell you straight away; he can't wait to tell you in person. So a lot of his instructions this time came in the form of e-mail.
Miyamoto Right, it was the first time I have done it through e-mail.
Aonuma When we were working on Wind Waker, he would simply hand me two-page documents with all his comments gathered together, saying: "There you go!"
Miyamoto: In the past I would often gather my comments in one document and hand them to the people in charge. I also used to make a point of avoiding going directly to the development area and to only deal with team leaders. That's because the management of the development team had been entrusted to them. This time round however, there were of course a huge number of people involved as well as a lot of young developers. That's why I thought that rather than all these instructions appearing out of nowhere, it was better if the developers could actually see the process behind these decisions.
http://iwataasks.nintendo.com/interviews/#/wii/twilight_princess/0/4
Iwata: Miyamoto-san, how did you feel when you became fully involved in the development process?
Miyamoto: That's a difficult one. I hope it's okay to speak frankly?
Iwata: By all means.
Miyamoto: Well, I've been involved in developing several prototypes throughout the course of the project, so there weren't any serious problems, but... Firstly, the leaders hadn't been checking the progress of the staff. Many staff members weren't able to properly execute the most fundamental parts of their assignments. They weren't able to play catch yet; in fact, they hadn't even got the gist, such as catching the ball in the middle of the glove... Sloppy work, you might say. That's why I've mostly been helping by explaining to them clearly so they could better understand what they are supposed to do in order to correctly execute their assignments. There's one thing I've been grateful for, and that is the level of motivation these people have. The cause of the sloppiness wasn't due to people's lack of motivation, but more that they were stuck in a rut due to the huge amount of work they had. Iwata I see. You could say they didn't know where to direct their focus? Miyamoto Yes, that's it. Because they were already highly motivated, simply by pointing out what task they should be doing, they were able to make significant progress. And so we've managed to finish in around four months what would have taken around half a year. I was a little concerned at first, but the level of motivation within the development team has really helped.
For Super Mario Galaxy Miyamoto worked as Producer and is responsible for the game design of using gravity and spherical worlds. He regularly evaluated Super Mario Galaxy and is also the reason they switched the life balance from 6 life points to 3.
http://iwataasks.nintendo.com/interviews/#/wii/super_mario_galaxy/3/2
Iwata: For this last interview, I would like to ask Miyamoto-san, the creator of Mario, and the person in charge of game design for Super Mario Galaxy.
Miyamoto: So what I had come up with, was gravity.
Gravity was used a lot in old movies, with things like being able to walk upside-down on the ceiling.
But if you think about it, nobody was really able to do that before in real life, and I though it would be great if I were able to recreate that in a game. People would be able to have a new experience, and it would be so much fun being able to play around in that kind of an environment.
But when I told that to the staff, they became worried, and asked me "Can we really call something like that a game?" So I told them, that if I were to make a game that was not fun, I would much rather make something that was not a game, but everyone would find a lot of fun! (laughs)
Miyamoto: It came down to finding the right idea. With a spherical field, you’re able to create new styles
from a design perspective, and this type of field is also good for the camera angles. So even after experimenting with Mario 128, I wanted to save it for another time.
Iwata: I felt that this was a very difficult project in the way you had participated.
You weren’t the director like in Mario 64, and even though you knew the staff in EAD Tokyo very well, it was about 400 kilometers (about 250 miles) away from Kyoto.
Miyamoto: But I think I was able to work in a pleasant environment.
I don’t think we would have been able to make this game if I was the director, getting my feet wet in the development process, but I think it was possible because I was the producer. The development tools we were using were so much better than the ones we used in the past; the computer on my desk was always connected to Tokyo. Iwata: You were connected to them so much, that even in the mornings on days off, you were emailing them! (laughs)
Miyamoto: They were constantly sending me the latest data, so I was able to respond to them immediately.
When I would go to Tokyo in the earlier stages of development,
I took over an entire room and had the development leads come in one by one, and we talked about the game while we were playing.
But then it struck me, "Is this something that I need to be doing all the way in Tokyo!?" (laughs) So I had the same environment created in one of the conference rooms in Kyoto, and I held meetings displaying the game screen using a camera, and talking about how we should change things in the game via video conferencing. So I was able to work as if I were in the Tokyo office.
Iwata: Koizumi-san, the director, referred to you playing the game as if you were sampling their first dishes that they had created.
Miyamoto on Star Fox Zero on being credited as a director for the first time in years.
http://www.nintendo.co.uk/News/2016/May/Star-Fox-Zero-Dev-Team-Interview-Part-Two-1107887.html
Sao: Listening to you speak, Miyamoto-san, it sounds like you were deeply involved in the development of this game.
Miyamoto: Well, I am credited as both producer and supervising director, and I’d say that what I did was pretty close to working as a director.
Sao: When did you last take on that kind of role?
Miyamoto: On The Legend of Zelda: Ocarina of Time, which came out in 1998, I was close to being a director, but was credited as a producer. So the last time I was credited as a director would have been before that, on Super Mario 64.