I really don't know. That's quite a good question. It would really be a great topic on Iwata Asks, even if Miyamoto wasn't there (He wouldn't be). He probably told the creators that they did a good job, because he wouldn't want to be mean. At least probably not. But he probably didn't like them very much at all. And I wonder why they released a third one after the first two, even if Miyamoto didn't like them. Maybe he did like them.. Or maybe he just said that the first two were good, so they made a third. But after that, he told them to stop. Unlikely. Hmm.
I suppose Miyamoto watched over Capcom making their Zelda games more because of the experience that he had with the CD-i games. For example, he made Capcom scrap FSA's story midway through development because it was "to confusing and complicated". That just shows that he was being more careful. I suppose that we will never really know however. Oh well.