Nintendo will likely go with the same NDS cart form factor (for backwards compatibility), only instead of using just flash storage they'll use holo storage for newer 3D games that will require higher capacities.
Next-Gen DS Card Patent
I had once thought that this would be for a universal format (that would also play in the next home console), but this 3DS really has thrown me...Nintendo seems to want to further wedge the difference between console & portable and keep them seperate lines. It would be very unlikely that their next home console would require 3D (go buy a new 3D TV or apply a goofy screen over your current one) just for some type of universal approach to both handhelds & home home consoles like I had once thought. This really could mean ANYTHING for the next Wii...possibly even holographic projection...or maybe they can possition the current (or future model) Wii as the at-home hub/network for their mobile gaming world domination plans with the next DS?
I have a theory that 3D isn't all that the next DS will be about, it's just what they're telling us (and the competition) for the time being in order to throw us all off even further when it's unveiled.