So I got the 3DS a few weeks ago and OOT. At first, the 3D effect at the higher settings made me cry, but I got used to it eventually. I still want to turn the device to use OOT's tilt aim, which of course ruins the 3D and makes you see double. Which is a pity, because aiming arrows is so much easier in 3D.
It gets me thinking, Pokédex 3D has faaar too much value invested in the quality of the models to be a stand-alone project. I think we may see a Colosseum or PBR style game sometime down the road on the 3DS using these models. (I doubt the main lineage of RPGs would abandon their sprite art any time soon since they would have done it already if they were going to.)