The GameCube really probably had Iwata more involved in it than Yamauchi. Yamauchi had stepped back from the company quite a bit by that time, the 64DD was kinda his swan song.
He returned to push the company in the direction of the DS/Wii though and mandated the whole blue ocean/easy to play/gamers don't want fancy graphics push in 2004 and then basically stepped back for good. Even Iwata has admitted they really only designed the DS to be the way it was because Yamauchi insisted on a two screen handheld ... just because, lol.
I kinda have to wonder if Yamauchi just had an uncanny "golden touch". He didn't really give a crap about video games, lol, but he seemed to have an uncanny sense of pushing the company in the right direction at just the right time.
The 3DS and Wii U were more or less developed primarily by Iwata and company but they don't seem to have the same "Yamauchi touch".