Nintendo has a myriad of problems with third parties.
One of them is the third party games that Nintendo fans tend to cry about not having the most (GTA, MGS, etc.) are not family games. So third parties don't really have much help from Nintendo at all in carving out this audience, Nintendo's attitude is basically "well you guys do all the work". Mario or Wii Fit U don't do much for the sales of a game like Crysis.
And Nintendo makes almost exclusively family-friendly style games. That's their entire portfolio. The only wrinkle they've added really is the casual gaming fad with things like fitness and music and mini-game fests taking off.
But under Iwata they've largely even scrapped trying to make games like Eternal Darkness, Perfect Dark, NBA Courtside, Conker's BFD, Ken Griffey Jr. MLB, the Star Wars Rogue Squadron games, etc.
It's never a problem for Nintendo to get a Sonic or Rayman or Skylanders or LEGO or Just Dance or Zumba Fitness game ... because these are brands that Nintendo's own IP pave the way for so publishers know there's an audience for that already (ie: Mario, Mario Kart, Wii Fit, Wii Sports, etc.).
