In the lastest "Iwata Asks" Interview session, Nintendo President, Satoru Iwata suggested that 3D video recording could come to the 3DS in "future updates." Bare in mind that Iwata-san didn't exactly mention what "updates" specifically alludes to. It could mean a simple software update that will add the video recording feature or it could mean the next iteration of the 3DS.
If Nintendo's console history is anything to by, 3D recording will mostly likely come from a hardware update. In the past, most of Nintendo's firmware updates have been for combatting piracy and homebrew hacks. None have really added anything new like the way Apple breathes new life into its iOS devices with new functions.
Guess you won't be filming your next homemade 3D Avatar anytime soon. At least you will still be able to take 3D photos with the 3DS. I wonder how stop-motion animations will be affected by 3D. What do you think?