In general, I agree with parts of the article, though perhaps for slightly different reasons. I wouldn't say Miyamoto is holding back the newer talent at Nintendo because, even though EAD Tokyo have been working on lots of Super Mario, they created the Galaxy games, as well as 3D Land and 3D World, or, to put that another way, the best Super Mario games ever made. While I understand the article's point about these games being overshadowed somewhat by the legacy of the series itself, I can't agree with the implication that it has been something of a waste of their obvious skills.
To be honest, my main gripe with Miyamoto that made me think it was time for him to step back and retire, or at least take on an almost entirely PR role, were comments he recently made regarding Starfox and F-Zero. Of Starfox, he said that the series would likely not continue since sales across the franchise were poor. I can understand that but his attitude is very defeatist. Starfox's sales only really began to slump once Nintendo started outsourcing it to the likes of Rare, Namco, and Q Games. At the very least I'd have expected him to want to give making his own Starfox another shot before writing off one of the company's most recognisable assests. Of F-Zero, he said that another game was unlikely simply because he had no new ideas for it. The entire franchise has hit a screeching dead end because he, personally, dosn't know what to do with it. All I can think is why doesn't he let the younger talent at Nintendo have a go? Just because he has no ideas doesn't mean nobody else does.
It's that sort of attitude, that he is the ultimate decider on IPs he created, that I feel has been the cause of several disappointments in recent years. Besides the indefinite stagnation of Starfox and F-Zero, Miyamoto is also responsible for the use of the Motion Plus in Skyward Sword. Aonuma has said in the past that he didn't want to use it but had to when Miyamoto insisted. I've said numerous times that Skyward Sword's short comings all stem from the over-reliance on the Wiimote, and I have Miyamoto to blame for that. Then there's the fact that the more recent IPs he's created haven't really been any good. Wii Sports was a huge hit, sure, but it was a party game that was played maybe three or four times a year, usually on special occassions. Wii Fit was only really popular with older women and people who believed that a light jog on the spot would make them skinny. Wii Music was a disaster. The last thing he created with lasting appeal was Pikmin. Over the last five or six years, he hasn't really been displaying much genuinely impressive creativity when it comes to creating new IPs (which is partially why I remain cautiously optimistic about this new one he's cooking up) and so I do feel as though it is time that he stepped back and let fresh talent take over his creations.
I don't agree with the assertion that Miyamoto is the source of Nintendo's current problems. I don't think it's fair to blame Iwata, either. Some people seem quick to forget that Iwata grew Nintendo into a company larger than it had ever been before, following the success of the Wii and DS, and the software output from Nintendo and its second-parties has been outstanding since the GameCube. Under his leadership, Nintendo products expanded video game's general audience and helped make gaming a more mainstream activity. He is good at his job. The problems the Wii U is facing are similar to those faced by the 3DS, and those problems were solved by pumping out quality games and advertising the crap out of it. While I'm still waiting on seeing some actual Wii U advertising (in the UK, there is basically nothing) the platform does now have a strong line-up of exclusives--3D World, The Wind Waker, Wonderful 101, Pikmin 3, ZombiU--with many more to come, including Donkey Kong, Hyrule Warriors, Mario Kart 8, Bayonetta 2, and Smash Bros. A big marketing push, maybe some generous bundle deals when Mario Kart is released, and I would also say a price drop could work wonders for the Wii U's sales and see it make the turn the 3DS did.
Nintendo's current problems, if you ask me, are the result of the company still being in the mind-set they fell into during the Wii years. While the games they produced in that time were mostly fantastic, there weren't very many of them, and there was little to no third-party support outside of shovelware. Nintendo didn't need to worry about building relationships with other developers, or having a new game every month, because they had so much money that their lives were carefree and without troubles. Now they have to work at being successful again. They've done a great job so far with the 3DS and if they can pull off similar with the Wii U then Nintendo will dig itself out of its current hole. I believe Iwata can get that done, and I believe Miyamoto can help him do that, albeit by letting go of some of his creations to enable them to flourish.