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This is like picking between 2 flavors of ice cream.  There are no wrong answers.  Both of these guys are heroes to me.

If I have to pick though, I'll say Iwata.  Yamauchi was a pioneer, and the NES was my favorite console.  Objectively, the NES has all of the games that you'd really want to play for Generation 3 anyway (or at least 99% of the games), and so many of the games were really innovative.  I doubt another console this glorious will ever be made.  However, Iwata was also brilliant and the DS, Wii and Switch are the 3 most innovative systems of the 21st century.  But the reason I'd have to give it to Iwata is that he was humble and Yamauchi was arrogant.  So personally, I have a bit more respect for Iwata, but I really admire the contributions both men have made to gaming.