In the current Iwata Asks Interview, Saturo Iwata clarifies 3D compatibility and the Nintendo 3DS. With the Nintendo 3DS, games can be played with different capabilities. It has been known that 3D can be turned off on games, and he also articulates that the device is compatible with older DS games as well. The inclusion of 3D capabilities in games are completely left up to the developer of the game, Iwata stated.
“New game cards, however, will be specific to Nintendo 3DS, but whether they will be in 3D or not is basically up to the maker, just like how much to use the touchscreen was up to developers for Nintendo DS.”
Realizing that the technology is new, and will take time to master. He expects that not all games developed for the 3DS will contain the 3D functionality, and that requiring software makers to adhere to a 3D only rule would limit the contributions to the handheld.
Source: Nintendo via Eurogamer