Looooooooong read about Inafune's reasons for leaving.
http://www.neogaf.com/forum/showthread.php?t=411847tldr: game companies need to stop being complacent with Japanese lifetime employment and make better games, one of the steps toward this is collaboration with western companies, Capcom wasn't helping him do that, and he wants Japanese devs to get recognition for the successes of a franchise instead of the current system of no recognition for success but all the blame for failure. He wanted to leave after Legends 3 was finished but he couldn't take it anymore. Also it's sorta a slap in the face of fans but he says that the game's gonna prove his point if it does well, saying if it does well it's because it's a Mega Man game and not an Inafune game. I think I worded that in a confusing way but yeah, read for all the details and insights into something I think a lot of westerners already think and Japanese don't.