I'm not sure you're really up to speed on this front Sky. You just can't compare the interesting twists you mentioned in Zelda to what Little Big Planet accomplished for user generated content on consoles or the storytelling risks taken by Heavy Rain and Beyond: Two Souls. And from what I understand, Flower and Journey were co-developed by Sony Santana Monica. Demon's Souls, arguably the most influential game of last generation, came about from a similar arrangement with Japan Studio.
If you want to make a case for Nintendo over Microsoft and Sony, innovation is not one of the categories you should pursue.