The main issue with going third party is losing licensing fee revenue.
Aside from the Wii U every Nintendo platform, even the GameCube, had significant amount of licensing revenue from third parties.
It doesn't even matter if a third party game sells or not ... that copy of Barbie's Dream Adventure sitting in the $10 discount bin for Wii or 3DS at your local Wal-Mart? Guess what? Nintendo already made $6-$10 for that copy of the game whether it sells or not because the publisher had to pay that fee just to have it manufactured.