Better to keep a money-making IP around *in case* they get their balls back.
I speculate policies get in the way of a humble act such as a company giving the rights to a single individual. Isn't the rights to a franchise usually something that is bought, btw? I doubt Inafune is rich enough to buy Mega Man.
Honestly the whole concept of "This person is the director and this person head that department and blah blah blah" isn't really a concept in the gaming world of yesteryear. Back in the early NES and partially SNES days, developers weren't people of interest. You got your name in the credits, but otherwise you didn't really have the creative ownership and cult of personality. You made the game for the company you worked for, and the company took full credit for it.
It wasn't till Miyamoto came around and changed the game for everyone, although it was still a hard sell in Japanese game development, as opposed to say western game developers on PCs. Even now companies tend to hold onto their IPs with that mentality. Hence the big drama between Konami and Kojima.