Miyamoto oversees many, many video games that Nintendo makes. Unfortunately, Nintendo is usually vague about how much involvement Miyamoto has in any given title, and it's easy to point the blame on someone else when something goes wrong. After all, he hasn't been credited as Director in years.
There are Nintendo third party-developed titles that he has overseen which have been sub-par, but that wouldn't really answer your call. Personally, I thought Nintendogs was trash, and he was General Producer for that, but you may not care for that example. Yoshi's Story? He was a supervisor on that. Perhaps my best example is his role as GP for the Pokemon Channel.
You're right, I don't have any really definitive examples. But frankly, it's unrealistic to think that even the best game designer will always make a winner. All I know for sure is that what I played was horrible and many others who played it agree with me. And guess what: that's what game impressions are all about--what the writer played. There better be a lot more to the game when I see it in stores if Nintendo wants me to change my tune.