Kerwrong! You forget that Retro also did roughly half of the character modelling and animations, submitted concepts for the new tracks (many of which were used in the final versions, though they didn't mention which ones) and they designed the DKCR track. EAD may have written the base engine, but Retro did far more than "just" the 16 classic tracks.
What are you the comic book guy from The Simpsons now? I gave the simplified Hideki Konno response. If you want a detailed summation:
+ EAD developed the technology inhouse (game engine, physics, online infrastructure)
+ EAD did the music
+ EAD responsible for all the course design (new and classic) (Read Below)
+ Retro mainly used for environment design and animation and some character models
+ Their biggest independent role was redesigning the environments of the classic tracks which already had the track layout done. They added extra routes (air, water right?) Which was the only track design they did but then it was edited again by EAD according to part 2.
Does Retro's role sound familiar? Iwata's Ask part 1 highlights their role which is not so different than how Monolith Soft assisted in Zelda. Retro handled the animations with EAD's character designer. Retro recreated the backgrounds of the classic EAD tracks. Suggested some concept designs for the EAD art team on the original courses. The only creative gameplay design I am reading, was that Retro got to design the courses of the shortcuts added to the classic stages. Which was still edited by EAD's director and course design team according to Iwata's Ask Part 2. Also follows what Miyamoto said in the interview.
The point is even in the co-developed games like Ocarina of Time (Grezzo) or Star Fox 64 3D (Q-Games). Or "assisted" games like Skyward Sword (Monolith) and Mario Kart 3D (Retro Studios). No one designs the courses / levels but EAD! NO ONE. They are either recreating the map EAD already made while EAD cooperates, or they are assisting around the confines of the EAD designed map. (Creating characters, objects, animating).
Correct me if my postulation is wrong. But this is currently how games at EAD are co-developed or collaborated on. If it was anything different, than it would probably fall under the SPD division more likely.
Confirmation that Miyamoto will be working with multiple small teams. Perhaps that means that he's heading to SPD, rather than setting up a new studio?
There is no way Miyamoto is working for SPD. It would be sacrilege. Iwata nor Miyamoto would allow him to work for Takahashi. It is against Japanese business culture entirely. It is either a new division entirely, or a new EAD group. I think it is the first one.