Well, ultimately, this is a business and in any good business, three years of losses would get most CEOs canned. It would be sad though, Iwata is easily likeable and I have always felt he is a true champions for the industry. I think the core values he holds for Nintendo are good ones.
I think he's stuck in a hard place. He is loyal to the principles that made Nintendo insanely rich and successful, which is what you'd expect him to do, but he I don't think he has adapted the company enough. The software drought for Wii U is inexcusable, especially so when you consider they suffered the exact same problems with 3DS.
On the positive side, you best believe Super Mario Wii U & Mario Kart are coming 2013.