What I forsee is some developers wanting to ignore the 3D capabilities. "I have two sets of consoles, one with 3D and the other without. Ditch the 3D!"
I probably won't happen because Nintendo is known to force the developers to use their gimmicks, but most of them are probably thinking about it.
I would also like some information about the hardware. Will it have the same processor and/or GPU? The 3d effect spends some resources, so will there be games that run better in the 2DS than on the 3DS?