First and foremost, a quick disclaimer: like the article mentioned, The Pokémon Company is not Nintendo, but an affiliate company created to manage the franchise's many tendrils like comics, TV shows, movies, merchandising etc. So this isn't even like Nintendo itself developed the software.
So, let's set the record straight: this is not a sign of anything, it is not a trend and it is most certainly not related to the current 3DS woes. I share Kohler's point of view: Nintendo's strength has always been its uniqueness. In fact, their recent success with the Wii and DS lies almost entirely on their courage to be different: the Blue Ocean Strategy to grow a stagnant market. OK, you can all lower your hands: yes, the mobile market also exploded, but while it may or may not be a bubble, the fact is that it is a ruthless and complex ecosystem. It's no wonder Apple itself is not producing games: while its very lucrative to run the App Store and nickel-and-dime content providers, making money as a developer has proved tricky and extremely unpredictable.
Now, by trying to shoehorn Nintendo software into the App Store, a bunch of problems start cropping up: they wouldn't get NEARLY as much attention as they do on their own platforms... but that's just the beginning. As Kohler pointed out, Nintendo fine tunes their hardware meticulously for their software - Apple forces draconian limitations on all content providers on a whim. And while Nintendo's production system run on very low costs, they iterate prototypes like crazy - I would assume between the time they start tinkering with a concept until they deliver a finished product, Apple will have gone through 3 major iOS updates and 2 iPhone revisions at least (true, that may also apply to their own hardware, but at the very least can plan much better by looking further ahead on their own hardware roadmap).
Can you even imagine Nintendo trying to bow down to the style of simplistic software that people consume on the App Store? While I think they are very capable developers, to me it feels like asking Beethoven to compose heavy metal or Leonardo da Vinci to draw an impressionist fresco - I am not making any judgements of value here, but the fact is that they developed their methods towards other styles.
So, at the end of the day, what does developing for the App Store (or any other mobile-focused marketplace, for that matter) entail for Nintendo?
- Way more competition and less ways of standing out
- Absolutely no control over hardware; external software limitations
- Fickle audience with a narrow focus on limited experiences (quick and cheap is better)
- Giving up on emerging opportunities of innovation
Sure, a lot has changed, and Nintendo is by no means a saint: they did a fair share of strong-arming software developers in the Famicom days, but they still see videogames as not only their future, but as a form of craft that needs to be preserved and cared for. And so far they seem to have done a good enough job to be trusted with this amazing medium.

