Since (roughly) the SNES generation, every new generation of hardware has resulted in development cost increases of 2 to 4 times the previous generation's development costs. The core reasons for this increase is that there is more work required to produce a single graphical asset and there are more graphical assets required to produce the higher detailed graphics associated with each generation.
Handheld games have (generally speaking) had much lower development costs than console games because the hardware is a couple of generations behind consoles, new tools and better procedures make creating graphical assets (at those quality levels) less time intensive, and handheld games are generally much smaller in scope than home console or PC games; but from generation to generation the costs associated with creating a handheld game have increased between 2 and 4 times what the previous generation's development costs were.
The 3DS having increased development costs isn't that much of a surprise, but I suspect a lot of developers will avoid having to deal with that by producing more traditional sprite based games rather than push the limit of the 3DS.