The industry is full of people who embrace these "story-driven" games, so of course his comment is going to be controversial on message boards. Don't think you're special for disagreeing with Miyamoto; You're run of the mill. He probably says these things knowing full well it's going to upset people. The fact that he even has to comment on this in the first place means story driven games have become popular, which means he knows he's "attacking" something a lot of people love.
He has free rights to express negative opinions of something popular. Just because he's popular himself doesn't take away this right, just because you want to keep imagining Miyamoto as some higher being who could never say anything you actually dislike.