Well, everybody, it's all over. Go on home.
Seriously though, who knows how many game-defining features were preserved through the development of a game due to Inafune being on the team. Mega Man is his baby and now it's in the hands of other people(then again, I'm certain his role in their development had diminished, I'm sure he had a lot of influence). Great parallel in the aforementioned Miyamoto. How would Mario and Zelda suffer without Miyamoto upending the tea table and checking for uncharacteristic elements because he knows his own character so well?
My friend tried to ease my concern by telling me that Inafune wanted ML3 to be 'up to the fans'(as seen in the recent design contests) but him dropping such a highly anticipated project is a slap in the face. He made claims for years that he always wanted to make ML3. I doubt he meant he just wanted it greenlit by the higher-ups so he could run out the door of Capcom. * le sigh*
At the end of the day, if he 'hated his job,' then I don't blame the guy for leaving. Go do what you want, Inafune. You deserve it.