Yamauchi earned that reputation for Nintendo. Then, Iwata inherited the problem and has been trying to mend it ever since without completely turning his back on the principles that made Nintendo the company they are today.
"No, no, dig up, stupid!"
I don't think it's necessarily fair that Nintendo is still paying for mistakes made over a decade ago, but they haven't found a strategy that works for everyone. It's not as simple as following the leader because then, they'll never be the leader. I think they're as close as they've ever been with Wii U though no one knows if that's good enough yet.