Nintendo has had an issue of not knowing how to design controllers ever since the N64.
It's the exact opposite. Nintendo designs their controllers for one or two specific games, and they usually fit them perfectly, to the detriment of every other game on the market.
While Sony and Microsoft have always tried to just build an average controller that's mostly well suited for every game, but never feels 100% suited for any one title. Just look at the ps3's analog face buttons which went so unused that most people don't even realize they
were analog. Because the 360 controller had full digital face buttons, and no developer was willing to implement what couldn't be done on both consoles. And now the ds4, which is otherwise a massive improvement over the old design, reverted back to digital face buttons.
Sony and Microsoft
can't innovate. Not because they're creatively bankrupt, but because those innovations come at a cost of third party development. Which we see time and again with Nintendo.
Plus there's that whole debate over symmetrical or asymmetrical sticks stems directly from whether the game being played is meant to be played with the left analog stick or d-pad as the primary movement control, where FPS fans tend to prefer the XBox layout while fighting game and retro sidescroller fans prefer the PlayStation layout. It's actually a point of contention with me that Nintendo opted to follow the XBox route when so much of their design mentality is rooted in the old school.