According to Andriasang's summary and translation of his blog post announcing the departure, Inafune declared he had no more "stairs" to climb within Capcom. "It would probably be good for me to sit gracefully in this seat and become a leading figure in the industry," he wrote. "However, I cannot do this. Settling down means death for a creator. As long as you are a creator, you cannot settle down." Inafune has been particularly unsettled lately, making frequent, harsh criticisms of the Japanese game industry, and (in what seemed like a frustrated joke at the time) declaring that he hated his job.
We think we know what happened here: It wasn't that Capcom higher-ups, uh, encouraged him out for his critical statements, or that Inafune received a more lucrative offer from one of the Western publishers he has become so fascinated with -- it's just that his Mega Man Legends 3 character design got last place.