Nintendo notes that since the DS launched just over three years ago, only 28 of the 50 titles that have shipped over a million were first party. That's still a sizable portion, but nowhere near the disparity found in its motion control-loving relative. As for the success of Nintendo's software, the report noted that internal teams have been familiar with and developing titles for the hardware for much longer than anyone else because they "know the Wii's special characteristics best."
The problem of third-party games and Nintendo consoles heralds as far back as the Nintendo 64 and was recently observed by No More Heroes creator Suda51. Of course, it's probably a lot more complicated than third-party developers growing more accustomed to the Wii's "special characteristics." It should be noted that, of the top 15 best-reviewed Wii games according to Metacritic, only six are from Nintendo.
[Image from Zack & Wiki: Quest for Barbaros' Treasure]