I think every hardware manufacturer does, except MS. Sony was notoriously hard to develop for as well since they had odd custom hardware every generation up to the PS4. SEGA was difficult to develop for. Nintendo has always had pretty difficult hardware (N64 anyone?)Nintendo does have a history of having hard to develop for consoles.
My comments RE: Sony really apply to both Nintendo's online capabilities and lacking SDK. Look at the PS3 library - many PS3 versions of cross platform titles were worse than the 360 counterparts yet all the first party titles were very impressive, so the problem was unlikely the hardware itself. And for most of the PS3's life, PSN was inferior to Xbox Live from what I understand. I don't own an Xbox so I can't directly compare the two, but MS has had the best online system for the last decade by far.
The real big problem here as I see it is that from what that article states, Nintendo did zero competitive analysis and didn't hire the right people to build their online system. Which is pretty inexcusable considering the console released in 2012, long after online play had been ubiquitous on every other console.