For your information, one person alone does not control the state of the company nor is it the sole reason why the company is suffering. Iwata was responsible for the great achievements of DS, Wii and 3DS sales and he's really a great person who is not part of the Nintendo-family blood. If at all, its encouraging them to hire more talented people and such and after the 3DS is doing wonders even without Hiroshi Yamuchi(Miss him dearly.....) I doubt that he should leave Nintendo ever. The Wii U will eventually have a system seller that will boom its sales.

This mostly happens on third party games since they tend to increase the quality of the game without checking for bugs and glitches most of the time. Just today when I was playing Lost World(3DS) in Desert Ruins 1, the game crashed for no reason. So far this is the only time it had crashed. I'm guessing that you need to update your 3DS frequently.