To be fair, Miyamoto was involved in both Metroid Prime and Star Fox Adventures although to what extent I'm not sure. It's obvious they were trying to take those series and make them more successful, but they dropped the ball. With Starfox, it started with changing Dinosaur Planet into Starfox Adventures. I think they had good intentions and saw the potential to help build the Starfox brand, but the gameplay in Adventures was such a departure from SF64, that it introduced major problems going forward. They tried to blend the two with Assault which just didn't work for multiple reasons. It was clear that after that they wanted to move the series back closer to its roots, but again they've never done it. Not one game in the series has controlled like the other.
The same thing happened with Metroid. After a rocky start, they semi-successfully translated the series into 3D. Like Starfox Assault, Other M was an attempt to blend two different gameplay mechanics into one. Both of these could have worked, but in both cases mistakes were made.
Here's what's important. Instead of Nintendo either correcting their mistakes or going back to what worked, they tried something new again with Starfox Zero and Metroid Federation Force further exasperating their problem and digging their hole deeper. The problem is that this doesn't apply to F-Zero. There is nothing wrong with the controls in F-Zero X or GX, yet Nintendo is still adamant on changing them.