No, he absolutely, unquestionably designed characters from scratch from the first game onwards.
Even the big shocking reveal that's supposed to prove that he's a hack--namely that he didn't direct the first two games and that he was only partially responsible for Mega Man's visual design--is something he freely admitted and the only reason so many people know about it is because he talked about it.
I don't think the dude is a hack, but I think he's given way more credit than is due. It's just when it comes down to "the only source is Inafune" there's not much room to move and you have no idea if it's dicky success-got-to-his-head Inafune finally trying to be humble after he realises he can't move mountains, or if it's just him trying to potentially pass blame for past misgivings.
I know he came into the project late. I know he's not the creator of Mega Man. I'm fairly certain he didn't get that "we'll just do what Inafune says" company culture until much later. He had a lot of rejected original designs. He didn't get things half his way until MMX, and totally his way until MMZ.
I don't believe Inafune is "just a business man", but I think he's a lot less better at what he does than people give him credit for. Not a hack, but just not great.