Also the Body Harvest situation ... that sounds like it was more of Miyamoto's call, he did not want the game to be action/violence centric, while DMA Design (Rockstar) wanted to go in that direction:
http://ca.ign.com/articles/2008/03/28/ign-presents-the-history-of-grand-theft-auto
Miyamoto basically did not approve and wanted the game to be more of a puzzle title. Take a wild guess who Nintendo sided with. I believe Buggie Boogie (supposed to be gritty car combat title) also went through a similar issue when Miyamoto wanted it to be more cartoony (ala Stunt Race FX). That game was cancelled outright.